Starting phenix.real_space_refine on Sun Mar 17 03:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/03_2024/6k9q_9952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/03_2024/6k9q_9952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/03_2024/6k9q_9952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/03_2024/6k9q_9952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/03_2024/6k9q_9952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/03_2024/6k9q_9952.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.165 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: 4 Type Number sf(0) Gaussians S 208 5.16 5 C 47317 2.51 5 N 13285 2.21 5 O 16092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "T ARG 105": "NH1" <-> "NH2" Residue "X TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 76902 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "B" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "C" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "D" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "E" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "F" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "G" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "H" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "I" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "J" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "K" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "L" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "M" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "N" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "O" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "P" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "Q" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 2952 Classifications: {'peptide': 401} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 388} Chain: "R" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "S" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "T" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "U" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "V" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "W" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "X" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "Y" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Chain: "Z" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2958 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 389} Time building chain proxies: 31.06, per 1000 atoms: 0.40 Number of scatterers: 76902 At special positions: 0 Unit cell: (185.393, 187.587, 239.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 208 16.00 O 16092 8.00 N 13285 7.00 C 47317 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: 23.06 Conformation dependent library (CDL) restraints added in 11.3 seconds 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18874 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 259 sheets defined 15.7% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 Processing helix chain 'A' and resid 366 through 400 removed outlier: 3.846A pdb=" N GLU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 366 through 401 removed outlier: 3.671A pdb=" N GLU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 25 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 367 through 400 removed outlier: 3.985A pdb=" N ILE C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 25 removed outlier: 3.532A pdb=" N SER D 7 " --> pdb=" O SER D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 177 removed outlier: 3.615A pdb=" N SER D 176 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR D 177 " --> pdb=" O ALA D 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 173 through 177' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 366 through 402 removed outlier: 4.180A pdb=" N ARG D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 Processing helix chain 'E' and resid 321 through 325 Processing helix chain 'E' and resid 366 through 400 removed outlier: 3.564A pdb=" N GLU E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 376 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 25 Processing helix chain 'F' and resid 173 through 177 removed outlier: 3.707A pdb=" N SER F 176 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 400 removed outlier: 4.229A pdb=" N ILE F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 25 Processing helix chain 'G' and resid 366 through 400 removed outlier: 4.472A pdb=" N ILE G 375 " --> pdb=" O LEU G 371 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL G 376 " --> pdb=" O VAL G 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 25 Processing helix chain 'H' and resid 366 through 400 removed outlier: 3.905A pdb=" N ILE H 375 " --> pdb=" O LEU H 371 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL H 376 " --> pdb=" O VAL H 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 25 Processing helix chain 'I' and resid 173 through 177 removed outlier: 3.730A pdb=" N TYR I 177 " --> pdb=" O ALA I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 325 removed outlier: 3.860A pdb=" N GLY I 324 " --> pdb=" O ASN I 321 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU I 325 " --> pdb=" O ASN I 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 321 through 325' Processing helix chain 'I' and resid 367 through 400 removed outlier: 4.058A pdb=" N ILE I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL I 376 " --> pdb=" O VAL I 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 25 Processing helix chain 'J' and resid 173 through 177 removed outlier: 3.513A pdb=" N TYR J 177 " --> pdb=" O ALA J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 400 removed outlier: 3.831A pdb=" N ILE J 375 " --> pdb=" O LEU J 371 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL J 376 " --> pdb=" O VAL J 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 25 Processing helix chain 'K' and resid 173 through 177 removed outlier: 4.048A pdb=" N TYR K 177 " --> pdb=" O ALA K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 400 removed outlier: 3.846A pdb=" N ILE K 375 " --> pdb=" O LEU K 371 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL K 376 " --> pdb=" O VAL K 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 25 Processing helix chain 'L' and resid 366 through 400 removed outlier: 3.562A pdb=" N GLU L 370 " --> pdb=" O ASP L 366 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE L 375 " --> pdb=" O LEU L 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 25 Processing helix chain 'M' and resid 173 through 177 removed outlier: 3.523A pdb=" N TYR M 177 " --> pdb=" O ALA M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 400 removed outlier: 3.717A pdb=" N GLU M 370 " --> pdb=" O ASP M 366 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE M 375 " --> pdb=" O LEU M 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 25 Processing helix chain 'N' and resid 173 through 177 removed outlier: 3.975A pdb=" N TYR N 177 " --> pdb=" O ALA N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 401 removed outlier: 3.844A pdb=" N GLU N 370 " --> pdb=" O ASP N 366 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE N 375 " --> pdb=" O LEU N 371 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL N 376 " --> pdb=" O VAL N 372 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 25 Processing helix chain 'O' and resid 366 through 400 removed outlier: 3.673A pdb=" N VAL O 376 " --> pdb=" O VAL O 372 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 25 Processing helix chain 'P' and resid 173 through 177 removed outlier: 3.707A pdb=" N TYR P 177 " --> pdb=" O ALA P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 366 through 400 removed outlier: 3.926A pdb=" N GLU P 370 " --> pdb=" O ASP P 366 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL P 376 " --> pdb=" O VAL P 372 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 25 Processing helix chain 'Q' and resid 366 through 400 removed outlier: 3.799A pdb=" N GLU Q 370 " --> pdb=" O ASP Q 366 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE Q 375 " --> pdb=" O LEU Q 371 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 25 Processing helix chain 'R' and resid 366 through 398 Processing helix chain 'S' and resid 2 through 25 Processing helix chain 'S' and resid 321 through 325 removed outlier: 3.552A pdb=" N GLY S 324 " --> pdb=" O ASN S 321 " (cutoff:3.500A) Processing helix chain 'S' and resid 336 through 340 removed outlier: 3.579A pdb=" N SER S 339 " --> pdb=" O THR S 336 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY S 340 " --> pdb=" O GLN S 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 336 through 340' Processing helix chain 'S' and resid 366 through 400 removed outlier: 4.146A pdb=" N GLU S 370 " --> pdb=" O ASP S 366 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE S 375 " --> pdb=" O LEU S 371 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL S 376 " --> pdb=" O VAL S 372 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN S 393 " --> pdb=" O LYS S 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN S 400 " --> pdb=" O ASN S 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 25 Processing helix chain 'T' and resid 321 through 325 removed outlier: 3.616A pdb=" N GLY T 324 " --> pdb=" O ASN T 321 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 340 removed outlier: 3.798A pdb=" N GLY T 340 " --> pdb=" O GLN T 337 " (cutoff:3.500A) Processing helix chain 'T' and resid 366 through 402 removed outlier: 4.109A pdb=" N VAL T 376 " --> pdb=" O VAL T 372 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG T 402 " --> pdb=" O LEU T 398 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 25 Processing helix chain 'U' and resid 366 through 399 removed outlier: 3.783A pdb=" N GLU U 370 " --> pdb=" O ASP U 366 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE U 375 " --> pdb=" O LEU U 371 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL U 376 " --> pdb=" O VAL U 372 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 25 Processing helix chain 'V' and resid 173 through 177 removed outlier: 3.664A pdb=" N TYR V 177 " --> pdb=" O ALA V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 366 through 399 removed outlier: 3.795A pdb=" N GLU V 370 " --> pdb=" O ASP V 366 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE V 375 " --> pdb=" O LEU V 371 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 26 removed outlier: 3.528A pdb=" N SER W 26 " --> pdb=" O ASN W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 321 through 325 Processing helix chain 'W' and resid 366 through 399 removed outlier: 4.368A pdb=" N ILE W 375 " --> pdb=" O LEU W 371 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL W 376 " --> pdb=" O VAL W 372 " (cutoff:3.500A) Processing helix chain 'W' and resid 400 through 402 No H-bonds generated for 'chain 'W' and resid 400 through 402' Processing helix chain 'X' and resid 2 through 25 Processing helix chain 'X' and resid 321 through 325 Processing helix chain 'X' and resid 366 through 401 removed outlier: 3.841A pdb=" N GLU X 370 " --> pdb=" O ASP X 366 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE X 375 " --> pdb=" O LEU X 371 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL X 376 " --> pdb=" O VAL X 372 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 25 Processing helix chain 'Y' and resid 321 through 325 removed outlier: 3.763A pdb=" N LEU Y 325 " --> pdb=" O ASN Y 322 " (cutoff:3.500A) Processing helix chain 'Y' and resid 336 through 340 removed outlier: 3.515A pdb=" N GLY Y 340 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 399 removed outlier: 4.113A pdb=" N ILE Y 375 " --> pdb=" O LEU Y 371 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL Y 376 " --> pdb=" O VAL Y 372 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 25 Processing helix chain 'Z' and resid 366 through 400 removed outlier: 3.548A pdb=" N GLU Z 370 " --> pdb=" O ASP Z 366 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN Z 400 " --> pdb=" O ASN Z 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 removed outlier: 6.010A pdb=" N THR A 35 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 56 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER A 37 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 5.317A pdb=" N ARG A 83 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 5.317A pdb=" N ARG A 83 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A 308 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR A 303 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL A 310 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A 301 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 312 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 290 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 101 removed outlier: 3.874A pdb=" N VAL A 108 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.710A pdb=" N THR A 126 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.928A pdb=" N THR A 150 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN A 280 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER A 152 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR A 278 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN A 154 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 156 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 274 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 186 removed outlier: 7.025A pdb=" N GLU A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER A 239 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 326 through 327 removed outlier: 3.967A pdb=" N ALA A 326 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 33 through 38 removed outlier: 3.837A pdb=" N SER B 33 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AB3, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 94 removed outlier: 5.622A pdb=" N ARG B 83 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 116 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 99 through 101 Processing sheet with id=AB6, first strand: chain 'B' and resid 243 through 246 removed outlier: 7.274A pdb=" N ASN B 156 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 275 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 179 through 186 removed outlier: 7.318A pdb=" N GLU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS B 230 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 291 through 293 removed outlier: 6.260A pdb=" N VAL B 299 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 316 through 318 removed outlier: 3.950A pdb=" N ASN B 318 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 326 through 327 Processing sheet with id=AC2, first strand: chain 'C' and resid 34 through 40 removed outlier: 5.715A pdb=" N THR C 35 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE C 56 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER C 37 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 65 through 67 Processing sheet with id=AC4, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.852A pdb=" N ARG C 83 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.852A pdb=" N ARG C 83 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 313 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL C 299 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 290 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AC7, first strand: chain 'C' and resid 242 through 246 removed outlier: 3.607A pdb=" N MET C 266 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 242 through 246 removed outlier: 6.552A pdb=" N ASN C 156 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C 275 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 179 through 186 removed outlier: 7.035A pdb=" N GLU C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 239 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 33 through 40 removed outlier: 6.845A pdb=" N SER D 33 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N THR D 35 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE D 56 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER D 37 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AD3, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AD4, first strand: chain 'D' and resid 134 through 135 removed outlier: 3.512A pdb=" N GLN D 313 " --> pdb=" O TYR D 118 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL D 299 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 134 through 135 removed outlier: 5.144A pdb=" N ARG D 83 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 334 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 326 " --> pdb=" O ALA D 334 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AD7, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=AD8, first strand: chain 'D' and resid 242 through 246 removed outlier: 7.186A pdb=" N THR D 150 " --> pdb=" O GLN D 280 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN D 280 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER D 152 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR D 278 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN D 154 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN D 274 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 179 through 186 removed outlier: 6.816A pdb=" N GLU D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS D 230 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 316 through 318 Processing sheet with id=AE2, first strand: chain 'E' and resid 33 through 40 removed outlier: 6.579A pdb=" N SER E 33 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR E 35 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE E 56 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER E 37 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AE4, first strand: chain 'E' and resid 75 through 77 removed outlier: 3.803A pdb=" N SER E 77 " --> pdb=" O LYS E 354 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS E 354 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 134 through 135 removed outlier: 5.536A pdb=" N ARG E 83 " --> pdb=" O THR E 116 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AE7, first strand: chain 'E' and resid 242 through 246 removed outlier: 7.458A pdb=" N MET E 266 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE E 155 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN E 268 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU E 157 " --> pdb=" O GLN E 268 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 242 through 246 removed outlier: 7.149A pdb=" N THR E 150 " --> pdb=" O GLN E 280 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN E 280 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER E 152 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR E 278 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN E 154 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 179 through 186 removed outlier: 7.023A pdb=" N GLU E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS E 230 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 290 through 293 Processing sheet with id=AF2, first strand: chain 'E' and resid 316 through 318 Processing sheet with id=AF3, first strand: chain 'F' and resid 34 through 40 removed outlier: 5.689A pdb=" N THR F 35 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE F 56 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER F 37 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AF5, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.608A pdb=" N THR F 356 " --> pdb=" O ALA F 75 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AF7, first strand: chain 'F' and resid 120 through 121 Processing sheet with id=AF8, first strand: chain 'F' and resid 242 through 246 removed outlier: 7.982A pdb=" N MET F 266 " --> pdb=" O MET F 153 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE F 155 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN F 268 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU F 157 " --> pdb=" O GLN F 268 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 242 through 246 removed outlier: 6.665A pdb=" N SER F 152 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR F 278 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN F 154 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 179 through 186 removed outlier: 7.152A pdb=" N GLU F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER F 239 " --> pdb=" O LYS F 230 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 290 through 293 removed outlier: 3.571A pdb=" N SER F 290 " --> pdb=" O ASN F 302 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL F 299 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 34 through 39 removed outlier: 6.159A pdb=" N THR G 35 " --> pdb=" O ILE G 56 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE G 56 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER G 37 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 65 through 66 Processing sheet with id=AG5, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AG6, first strand: chain 'G' and resid 91 through 94 removed outlier: 5.446A pdb=" N ARG G 83 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 91 through 94 removed outlier: 5.446A pdb=" N ARG G 83 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN G 313 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL G 299 " --> pdb=" O LEU G 311 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER G 290 " --> pdb=" O ASN G 302 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=AG9, first strand: chain 'G' and resid 242 through 246 removed outlier: 8.263A pdb=" N MET G 266 " --> pdb=" O MET G 153 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE G 155 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN G 268 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU G 157 " --> pdb=" O GLN G 268 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 242 through 246 removed outlier: 3.525A pdb=" N ALA G 277 " --> pdb=" O GLN G 154 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN G 156 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE G 275 " --> pdb=" O ASN G 156 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 179 through 186 removed outlier: 7.148A pdb=" N GLU G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS G 230 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 316 through 318 Processing sheet with id=AH4, first strand: chain 'G' and resid 326 through 327 Processing sheet with id=AH5, first strand: chain 'H' and resid 34 through 40 removed outlier: 5.694A pdb=" N THR H 35 " --> pdb=" O ILE H 56 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE H 56 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER H 37 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 65 through 67 Processing sheet with id=AH7, first strand: chain 'H' and resid 75 through 76 Processing sheet with id=AH8, first strand: chain 'H' and resid 134 through 135 removed outlier: 3.855A pdb=" N GLN H 313 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN H 309 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY H 301 " --> pdb=" O GLN H 309 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL H 299 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER H 290 " --> pdb=" O ASN H 302 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 134 through 135 removed outlier: 5.323A pdb=" N ARG H 83 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA H 326 " --> pdb=" O ALA H 334 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 120 through 121 removed outlier: 3.689A pdb=" N THR H 126 " --> pdb=" O THR H 121 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 242 through 246 removed outlier: 7.146A pdb=" N THR H 150 " --> pdb=" O GLN H 280 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLN H 280 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER H 152 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR H 278 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN H 154 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 179 through 186 removed outlier: 7.313A pdb=" N GLU H 206 " --> pdb=" O THR H 202 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER H 239 " --> pdb=" O LYS H 230 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 316 through 318 Processing sheet with id=AI5, first strand: chain 'I' and resid 33 through 40 removed outlier: 6.530A pdb=" N SER I 33 " --> pdb=" O GLN I 58 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN I 58 " --> pdb=" O SER I 33 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR I 35 " --> pdb=" O ILE I 56 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE I 56 " --> pdb=" O THR I 35 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER I 37 " --> pdb=" O ALA I 54 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 65 through 67 Processing sheet with id=AI7, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AI8, first strand: chain 'I' and resid 91 through 94 removed outlier: 5.090A pdb=" N ARG I 83 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.778A pdb=" N ARG I 83 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL I 315 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 12.222A pdb=" N VAL I 85 " --> pdb=" O GLN I 313 " (cutoff:3.500A) removed outlier: 14.964A pdb=" N GLN I 313 " --> pdb=" O VAL I 85 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 134 through 135 removed outlier: 15.806A pdb=" N GLN I 114 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 12.517A pdb=" N ALA I 317 " --> pdb=" O GLN I 114 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR I 116 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL I 315 " --> pdb=" O THR I 116 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN I 313 " --> pdb=" O TYR I 118 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL I 299 " --> pdb=" O LEU I 311 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 100 through 101 Processing sheet with id=AJ3, first strand: chain 'I' and resid 120 through 121 removed outlier: 3.775A pdb=" N THR I 121 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR I 126 " --> pdb=" O THR I 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'I' and resid 242 through 246 removed outlier: 8.015A pdb=" N MET I 266 " --> pdb=" O MET I 153 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE I 155 " --> pdb=" O MET I 266 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLN I 268 " --> pdb=" O ILE I 155 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU I 157 " --> pdb=" O GLN I 268 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'I' and resid 242 through 246 removed outlier: 7.504A pdb=" N THR I 150 " --> pdb=" O GLN I 280 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN I 280 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER I 152 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR I 278 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN I 154 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 179 through 186 removed outlier: 7.169A pdb=" N GLU I 206 " --> pdb=" O THR I 202 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS I 230 " --> pdb=" O GLU I 238 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'I' and resid 326 through 327 Processing sheet with id=AJ8, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.816A pdb=" N THR J 35 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE J 56 " --> pdb=" O THR J 35 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER J 37 " --> pdb=" O ALA J 54 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'J' and resid 65 through 67 Processing sheet with id=AK1, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AK2, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AK3, first strand: chain 'J' and resid 316 through 317 removed outlier: 15.728A pdb=" N PHE J 81 " --> pdb=" O TYR J 118 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N TYR J 118 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG J 83 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA J 120 " --> pdb=" O LEU J 311 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU J 311 " --> pdb=" O ALA J 120 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL J 310 " --> pdb=" O GLY J 301 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY J 301 " --> pdb=" O VAL J 310 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY J 312 " --> pdb=" O VAL J 299 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 91 through 94 removed outlier: 15.728A pdb=" N PHE J 81 " --> pdb=" O TYR J 118 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N TYR J 118 " --> pdb=" O PHE J 81 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG J 83 " --> pdb=" O THR J 116 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'J' and resid 134 through 135 Processing sheet with id=AK6, first strand: chain 'J' and resid 99 through 100 Processing sheet with id=AK7, first strand: chain 'J' and resid 242 through 246 Processing sheet with id=AK8, first strand: chain 'J' and resid 242 through 246 removed outlier: 7.294A pdb=" N THR J 150 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN J 280 " --> pdb=" O THR J 150 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER J 152 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR J 278 " --> pdb=" O SER J 152 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN J 154 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'J' and resid 179 through 186 removed outlier: 7.144A pdb=" N GLU J 206 " --> pdb=" O THR J 202 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER J 239 " --> pdb=" O LYS J 230 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'K' and resid 33 through 40 removed outlier: 6.486A pdb=" N SER K 33 " --> pdb=" O GLN K 58 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN K 58 " --> pdb=" O SER K 33 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR K 35 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE K 56 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER K 37 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'K' and resid 65 through 67 Processing sheet with id=AL3, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AL4, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AL5, first strand: chain 'K' and resid 99 through 101 Processing sheet with id=AL6, first strand: chain 'K' and resid 117 through 118 removed outlier: 6.432A pdb=" N VAL K 310 " --> pdb=" O GLY K 301 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY K 301 " --> pdb=" O VAL K 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY K 312 " --> pdb=" O VAL K 299 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'K' and resid 120 through 121 removed outlier: 3.779A pdb=" N THR K 121 " --> pdb=" O THR K 126 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR K 126 " --> pdb=" O THR K 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'K' and resid 242 through 246 removed outlier: 6.795A pdb=" N ALA K 151 " --> pdb=" O SER K 261 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'K' and resid 242 through 246 removed outlier: 6.795A pdb=" N ALA K 151 " --> pdb=" O SER K 261 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR K 150 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN K 280 " --> pdb=" O THR K 150 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER K 152 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR K 278 " --> pdb=" O SER K 152 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN K 154 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN K 274 " --> pdb=" O ASN K 156 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'K' and resid 179 through 186 removed outlier: 7.353A pdb=" N GLU K 206 " --> pdb=" O THR K 202 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'K' and resid 316 through 318 Processing sheet with id=AM3, first strand: chain 'K' and resid 326 through 327 Processing sheet with id=AM4, first strand: chain 'L' and resid 34 through 39 removed outlier: 5.549A pdb=" N THR L 35 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE L 56 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER L 37 " --> pdb=" O ALA L 54 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'L' and resid 65 through 66 Processing sheet with id=AM6, first strand: chain 'L' and resid 134 through 135 removed outlier: 5.515A pdb=" N ARG L 83 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N TYR L 118 " --> pdb=" O PHE L 81 " (cutoff:3.500A) removed outlier: 16.071A pdb=" N PHE L 81 " --> pdb=" O TYR L 118 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'L' and resid 290 through 293 removed outlier: 6.419A pdb=" N VAL L 299 " --> pdb=" O LEU L 311 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG L 83 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N TYR L 118 " --> pdb=" O PHE L 81 " (cutoff:3.500A) removed outlier: 16.071A pdb=" N PHE L 81 " --> pdb=" O TYR L 118 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'L' and resid 99 through 100 Processing sheet with id=AM9, first strand: chain 'L' and resid 120 through 121 removed outlier: 3.706A pdb=" N THR L 121 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR L 126 " --> pdb=" O THR L 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM9 Processing sheet with id=AN1, first strand: chain 'L' and resid 242 through 246 Processing sheet with id=AN2, first strand: chain 'L' and resid 242 through 246 removed outlier: 6.571A pdb=" N SER L 152 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR L 278 " --> pdb=" O SER L 152 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN L 154 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'L' and resid 179 through 186 removed outlier: 7.046A pdb=" N GLU L 206 " --> pdb=" O THR L 202 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'M' and resid 33 through 40 removed outlier: 6.573A pdb=" N SER M 33 " --> pdb=" O GLN M 58 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN M 58 " --> pdb=" O SER M 33 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR M 35 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE M 56 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER M 37 " --> pdb=" O ALA M 54 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'M' and resid 65 through 66 Processing sheet with id=AN6, first strand: chain 'M' and resid 75 through 76 Processing sheet with id=AN7, first strand: chain 'M' and resid 134 through 135 removed outlier: 6.713A pdb=" N VAL M 299 " --> pdb=" O LEU M 311 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'M' and resid 134 through 135 removed outlier: 5.031A pdb=" N ARG M 83 " --> pdb=" O THR M 116 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'M' and resid 120 through 121 removed outlier: 3.781A pdb=" N THR M 121 " --> pdb=" O THR M 126 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR M 126 " --> pdb=" O THR M 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN9 Processing sheet with id=AO1, first strand: chain 'M' and resid 242 through 246 removed outlier: 7.858A pdb=" N MET M 266 " --> pdb=" O MET M 153 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE M 155 " --> pdb=" O MET M 266 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN M 268 " --> pdb=" O ILE M 155 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU M 157 " --> pdb=" O GLN M 268 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'M' and resid 242 through 246 removed outlier: 3.654A pdb=" N ALA M 277 " --> pdb=" O GLN M 154 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN M 156 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE M 275 " --> pdb=" O ASN M 156 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'M' and resid 179 through 186 removed outlier: 7.141A pdb=" N GLU M 206 " --> pdb=" O THR M 202 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS M 230 " --> pdb=" O GLU M 238 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'M' and resid 316 through 318 removed outlier: 3.639A pdb=" N ASN M 318 " --> pdb=" O LEU M 343 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'N' and resid 34 through 40 removed outlier: 6.123A pdb=" N THR N 35 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE N 56 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER N 37 " --> pdb=" O ALA N 54 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'N' and resid 65 through 67 Processing sheet with id=AO7, first strand: chain 'N' and resid 75 through 76 removed outlier: 3.890A pdb=" N THR N 356 " --> pdb=" O ALA N 75 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'N' and resid 91 through 94 Processing sheet with id=AO9, first strand: chain 'N' and resid 99 through 100 Processing sheet with id=AP1, first strand: chain 'N' and resid 117 through 118 removed outlier: 6.492A pdb=" N VAL N 299 " --> pdb=" O LEU N 311 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER N 290 " --> pdb=" O ASN N 302 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'N' and resid 242 through 246 removed outlier: 7.597A pdb=" N THR N 150 " --> pdb=" O GLN N 280 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN N 280 " --> pdb=" O THR N 150 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER N 152 " --> pdb=" O THR N 278 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR N 278 " --> pdb=" O SER N 152 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN N 154 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'N' and resid 179 through 186 removed outlier: 7.149A pdb=" N GLU N 206 " --> pdb=" O THR N 202 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS N 230 " --> pdb=" O GLU N 238 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'N' and resid 316 through 318 Processing sheet with id=AP5, first strand: chain 'N' and resid 326 through 327 Processing sheet with id=AP6, first strand: chain 'O' and resid 33 through 39 removed outlier: 4.023A pdb=" N SER O 33 " --> pdb=" O ASP O 59 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA O 39 " --> pdb=" O VAL O 53 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL O 53 " --> pdb=" O ALA O 39 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'O' and resid 65 through 67 Processing sheet with id=AP8, first strand: chain 'O' and resid 75 through 76 Processing sheet with id=AP9, first strand: chain 'O' and resid 326 through 328 removed outlier: 3.557A pdb=" N ALA O 326 " --> pdb=" O ALA O 334 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL O 332 " --> pdb=" O GLN O 328 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG O 83 " --> pdb=" O THR O 116 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'O' and resid 326 through 328 removed outlier: 3.557A pdb=" N ALA O 326 " --> pdb=" O ALA O 334 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL O 332 " --> pdb=" O GLN O 328 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG O 83 " --> pdb=" O VAL O 315 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL O 315 " --> pdb=" O ARG O 83 " (cutoff:3.500A) removed outlier: 12.046A pdb=" N VAL O 85 " --> pdb=" O GLN O 313 " (cutoff:3.500A) removed outlier: 15.510A pdb=" N GLN O 313 " --> pdb=" O VAL O 85 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'O' and resid 134 through 135 removed outlier: 16.207A pdb=" N GLN O 114 " --> pdb=" O ALA O 317 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N ALA O 317 " --> pdb=" O GLN O 114 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR O 116 " --> pdb=" O VAL O 315 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL O 315 " --> pdb=" O THR O 116 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN O 309 " --> pdb=" O GLY O 301 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY O 301 " --> pdb=" O GLN O 309 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL O 299 " --> pdb=" O LEU O 311 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=AQ4, first strand: chain 'O' and resid 120 through 121 removed outlier: 3.920A pdb=" N THR O 126 " --> pdb=" O THR O 121 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'O' and resid 242 through 246 removed outlier: 8.443A pdb=" N MET O 266 " --> pdb=" O MET O 153 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE O 155 " --> pdb=" O MET O 266 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN O 268 " --> pdb=" O ILE O 155 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU O 157 " --> pdb=" O GLN O 268 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'O' and resid 242 through 246 removed outlier: 7.155A pdb=" N THR O 150 " --> pdb=" O GLN O 280 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN O 280 " --> pdb=" O THR O 150 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER O 152 " --> pdb=" O THR O 278 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR O 278 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN O 154 " --> pdb=" O VAL O 276 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'O' and resid 179 through 186 removed outlier: 7.163A pdb=" N GLU O 206 " --> pdb=" O THR O 202 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'P' and resid 34 through 41 removed outlier: 5.899A pdb=" N THR P 35 " --> pdb=" O ILE P 56 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE P 56 " --> pdb=" O THR P 35 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER P 37 " --> pdb=" O ALA P 54 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY P 50 " --> pdb=" O MET P 41 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'P' and resid 65 through 67 Processing sheet with id=AR1, first strand: chain 'P' and resid 91 through 94 removed outlier: 5.150A pdb=" N ARG P 83 " --> pdb=" O THR P 116 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'P' and resid 91 through 94 removed outlier: 5.150A pdb=" N ARG P 83 " --> pdb=" O THR P 116 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL P 310 " --> pdb=" O GLY P 301 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY P 301 " --> pdb=" O VAL P 310 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY P 312 " --> pdb=" O VAL P 299 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'P' and resid 100 through 101 Processing sheet with id=AR4, first strand: chain 'P' and resid 242 through 246 removed outlier: 8.186A pdb=" N MET P 266 " --> pdb=" O MET P 153 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE P 155 " --> pdb=" O MET P 266 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN P 268 " --> pdb=" O ILE P 155 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU P 157 " --> pdb=" O GLN P 268 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'P' and resid 242 through 246 removed outlier: 6.708A pdb=" N SER P 152 " --> pdb=" O THR P 278 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR P 278 " --> pdb=" O SER P 152 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN P 154 " --> pdb=" O VAL P 276 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'P' and resid 179 through 186 removed outlier: 7.117A pdb=" N GLU P 206 " --> pdb=" O THR P 202 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'P' and resid 316 through 319 Processing sheet with id=AR8, first strand: chain 'P' and resid 325 through 327 Processing sheet with id=AR9, first strand: chain 'Q' and resid 33 through 40 removed outlier: 3.944A pdb=" N SER Q 33 " --> pdb=" O ASP Q 59 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA Q 39 " --> pdb=" O VAL Q 53 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL Q 53 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'Q' and resid 65 through 67 Processing sheet with id=AS2, first strand: chain 'Q' and resid 91 through 94 removed outlier: 4.895A pdb=" N ARG Q 83 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR Q 116 " --> pdb=" O ARG Q 83 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'Q' and resid 120 through 121 Processing sheet with id=AS4, first strand: chain 'Q' and resid 242 through 246 removed outlier: 7.955A pdb=" N MET Q 266 " --> pdb=" O MET Q 153 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE Q 155 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN Q 268 " --> pdb=" O ILE Q 155 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU Q 157 " --> pdb=" O GLN Q 268 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'Q' and resid 242 through 246 removed outlier: 7.344A pdb=" N THR Q 150 " --> pdb=" O GLN Q 280 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN Q 280 " --> pdb=" O THR Q 150 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER Q 152 " --> pdb=" O THR Q 278 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR Q 278 " --> pdb=" O SER Q 152 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN Q 154 " --> pdb=" O VAL Q 276 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'Q' and resid 179 through 186 removed outlier: 7.212A pdb=" N GLU Q 206 " --> pdb=" O THR Q 202 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS Q 230 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'Q' and resid 288 through 293 removed outlier: 6.022A pdb=" N VAL Q 299 " --> pdb=" O LEU Q 311 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'Q' and resid 315 through 318 Processing sheet with id=AS9, first strand: chain 'R' and resid 34 through 41 removed outlier: 5.904A pdb=" N ALA R 39 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL R 53 " --> pdb=" O ALA R 39 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET R 41 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL R 51 " --> pdb=" O MET R 41 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AT2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AT3, first strand: chain 'R' and resid 91 through 94 removed outlier: 5.333A pdb=" N ARG R 83 " --> pdb=" O THR R 116 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'R' and resid 91 through 94 removed outlier: 5.333A pdb=" N ARG R 83 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN R 309 " --> pdb=" O GLY R 301 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL R 299 " --> pdb=" O LEU R 311 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'R' and resid 99 through 101 Processing sheet with id=AT6, first strand: chain 'R' and resid 120 through 121 Processing sheet with id=AT7, first strand: chain 'R' and resid 242 through 246 Processing sheet with id=AT8, first strand: chain 'R' and resid 242 through 246 removed outlier: 3.583A pdb=" N ALA R 277 " --> pdb=" O GLN R 154 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN R 156 " --> pdb=" O ILE R 275 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE R 275 " --> pdb=" O ASN R 156 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'R' and resid 179 through 186 removed outlier: 6.953A pdb=" N GLU R 206 " --> pdb=" O THR R 202 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'R' and resid 326 through 327 removed outlier: 3.647A pdb=" N ALA R 326 " --> pdb=" O ALA R 334 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'S' and resid 33 through 38 removed outlier: 4.326A pdb=" N SER S 33 " --> pdb=" O ASP S 59 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'S' and resid 65 through 67 Processing sheet with id=AU4, first strand: chain 'S' and resid 75 through 76 Processing sheet with id=AU5, first strand: chain 'S' and resid 134 through 135 removed outlier: 3.983A pdb=" N GLN S 307 " --> pdb=" O TYR S 303 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL S 299 " --> pdb=" O LEU S 311 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'S' and resid 134 through 135 removed outlier: 5.292A pdb=" N ARG S 83 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA S 334 " --> pdb=" O ALA S 326 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 'S' and resid 99 through 101 Processing sheet with id=AU8, first strand: chain 'S' and resid 120 through 121 Processing sheet with id=AU9, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.443A pdb=" N ASN S 156 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE S 275 " --> pdb=" O ASN S 156 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'S' and resid 179 through 186 removed outlier: 6.994A pdb=" N GLU S 206 " --> pdb=" O THR S 202 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER S 239 " --> pdb=" O LYS S 230 " (cutoff:3.500A) Processing sheet with id=AV2, first strand: chain 'S' and resid 316 through 317 removed outlier: 3.550A pdb=" N LEU S 316 " --> pdb=" O GLY S 345 " (cutoff:3.500A) Processing sheet with id=AV3, first strand: chain 'T' and resid 34 through 41 removed outlier: 6.099A pdb=" N ALA T 39 " --> pdb=" O VAL T 53 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL T 53 " --> pdb=" O ALA T 39 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N MET T 41 " --> pdb=" O VAL T 51 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL T 51 " --> pdb=" O MET T 41 " (cutoff:3.500A) Processing sheet with id=AV4, first strand: chain 'T' and resid 65 through 66 Processing sheet with id=AV5, first strand: chain 'T' and resid 75 through 76 Processing sheet with id=AV6, first strand: chain 'T' and resid 82 through 85 Processing sheet with id=AV7, first strand: chain 'T' and resid 99 through 101 Processing sheet with id=AV8, first strand: chain 'T' and resid 134 through 135 removed outlier: 6.416A pdb=" N VAL T 299 " --> pdb=" O LEU T 311 " (cutoff:3.500A) Processing sheet with id=AV9, first strand: chain 'T' and resid 120 through 121 removed outlier: 3.903A pdb=" N THR T 126 " --> pdb=" O THR T 121 " (cutoff:3.500A) Processing sheet with id=AW1, first strand: chain 'T' and resid 242 through 246 Processing sheet with id=AW2, first strand: chain 'T' and resid 242 through 246 removed outlier: 6.926A pdb=" N ASN T 156 " --> pdb=" O ILE T 275 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE T 275 " --> pdb=" O ASN T 156 " (cutoff:3.500A) Processing sheet with id=AW3, first strand: chain 'T' and resid 179 through 186 removed outlier: 6.969A pdb=" N GLU T 206 " --> pdb=" O THR T 202 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS T 230 " --> pdb=" O GLU T 238 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'T' and resid 316 through 318 Processing sheet with id=AW5, first strand: chain 'U' and resid 34 through 40 removed outlier: 6.164A pdb=" N THR U 35 " --> pdb=" O ILE U 56 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE U 56 " --> pdb=" O THR U 35 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER U 37 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing sheet with id=AW6, first strand: chain 'U' and resid 65 through 66 Processing sheet with id=AW7, first strand: chain 'U' and resid 75 through 76 Processing sheet with id=AW8, first strand: chain 'U' and resid 91 through 94 removed outlier: 5.349A pdb=" N ARG U 83 " --> pdb=" O THR U 116 " (cutoff:3.500A) Processing sheet with id=AW9, first strand: chain 'U' and resid 91 through 94 removed outlier: 5.349A pdb=" N ARG U 83 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN U 313 " --> pdb=" O TYR U 118 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL U 310 " --> pdb=" O GLY U 301 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLY U 301 " --> pdb=" O VAL U 310 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY U 312 " --> pdb=" O VAL U 299 " (cutoff:3.500A) Processing sheet with id=AX1, first strand: chain 'U' and resid 242 through 246 removed outlier: 7.265A pdb=" N MET U 266 " --> pdb=" O MET U 153 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE U 155 " --> pdb=" O MET U 266 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN U 268 " --> pdb=" O ILE U 155 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU U 157 " --> pdb=" O GLN U 268 " (cutoff:3.500A) Processing sheet with id=AX2, first strand: chain 'U' and resid 242 through 246 removed outlier: 7.283A pdb=" N THR U 150 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN U 280 " --> pdb=" O THR U 150 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER U 152 " --> pdb=" O THR U 278 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR U 278 " --> pdb=" O SER U 152 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN U 154 " --> pdb=" O VAL U 276 " (cutoff:3.500A) Processing sheet with id=AX3, first strand: chain 'U' and resid 179 through 186 removed outlier: 6.984A pdb=" N GLU U 206 " --> pdb=" O THR U 202 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS U 230 " --> pdb=" O GLU U 238 " (cutoff:3.500A) Processing sheet with id=AX4, first strand: chain 'U' and resid 326 through 327 Processing sheet with id=AX5, first strand: chain 'V' and resid 34 through 40 removed outlier: 6.160A pdb=" N THR V 35 " --> pdb=" O ILE V 56 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE V 56 " --> pdb=" O THR V 35 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER V 37 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing sheet with id=AX6, first strand: chain 'V' and resid 65 through 67 Processing sheet with id=AX7, first strand: chain 'V' and resid 75 through 76 Processing sheet with id=AX8, first strand: chain 'V' and resid 126 through 127 removed outlier: 4.170A pdb=" N ALA V 120 " --> pdb=" O LEU V 311 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU V 311 " --> pdb=" O ALA V 120 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL V 310 " --> pdb=" O GLY V 301 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLY V 301 " --> pdb=" O VAL V 310 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY V 312 " --> pdb=" O VAL V 299 " (cutoff:3.500A) Processing sheet with id=AX9, first strand: chain 'V' and resid 134 through 135 removed outlier: 3.572A pdb=" N ALA V 326 " --> pdb=" O ALA V 334 " (cutoff:3.500A) Processing sheet with id=AY1, first strand: chain 'V' and resid 242 through 246 removed outlier: 6.934A pdb=" N GLN V 268 " --> pdb=" O ILE V 155 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU V 157 " --> pdb=" O GLN V 268 " (cutoff:3.500A) Processing sheet with id=AY2, first strand: chain 'V' and resid 242 through 246 removed outlier: 6.625A pdb=" N ASN V 156 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE V 275 " --> pdb=" O ASN V 156 " (cutoff:3.500A) Processing sheet with id=AY3, first strand: chain 'V' and resid 179 through 186 removed outlier: 7.374A pdb=" N GLU V 206 " --> pdb=" O THR V 202 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS V 230 " --> pdb=" O GLU V 238 " (cutoff:3.500A) Processing sheet with id=AY4, first strand: chain 'W' and resid 34 through 37 Processing sheet with id=AY5, first strand: chain 'W' and resid 126 through 127 removed outlier: 3.640A pdb=" N THR W 121 " --> pdb=" O THR W 126 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA W 120 " --> pdb=" O LEU W 311 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU W 311 " --> pdb=" O ALA W 120 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL W 310 " --> pdb=" O GLY W 301 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY W 301 " --> pdb=" O VAL W 310 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY W 312 " --> pdb=" O VAL W 299 " (cutoff:3.500A) Processing sheet with id=AY6, first strand: chain 'W' and resid 134 through 135 Processing sheet with id=AY7, first strand: chain 'W' and resid 99 through 101 Processing sheet with id=AY8, first strand: chain 'W' and resid 242 through 246 removed outlier: 6.772A pdb=" N ALA W 151 " --> pdb=" O SER W 261 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N MET W 266 " --> pdb=" O MET W 153 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE W 155 " --> pdb=" O MET W 266 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN W 268 " --> pdb=" O ILE W 155 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU W 157 " --> pdb=" O GLN W 268 " (cutoff:3.500A) Processing sheet with id=AY9, first strand: chain 'W' and resid 242 through 246 removed outlier: 6.772A pdb=" N ALA W 151 " --> pdb=" O SER W 261 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN W 156 " --> pdb=" O ILE W 275 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE W 275 " --> pdb=" O ASN W 156 " (cutoff:3.500A) Processing sheet with id=AZ1, first strand: chain 'W' and resid 179 through 186 removed outlier: 7.070A pdb=" N GLU W 206 " --> pdb=" O THR W 202 " (cutoff:3.500A) Processing sheet with id=AZ2, first strand: chain 'X' and resid 34 through 39 removed outlier: 6.328A pdb=" N ALA X 39 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL X 53 " --> pdb=" O ALA X 39 " (cutoff:3.500A) Processing sheet with id=AZ3, first strand: chain 'X' and resid 65 through 66 Processing sheet with id=AZ4, first strand: chain 'X' and resid 75 through 76 Processing sheet with id=AZ5, first strand: chain 'X' and resid 134 through 135 removed outlier: 3.607A pdb=" N TYR X 118 " --> pdb=" O GLN X 313 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN X 313 " --> pdb=" O TYR X 118 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N VAL X 299 " --> pdb=" O LEU X 311 " (cutoff:3.500A) Processing sheet with id=AZ6, first strand: chain 'X' and resid 134 through 135 removed outlier: 4.080A pdb=" N THR X 116 " --> pdb=" O ARG X 83 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG X 83 " --> pdb=" O THR X 116 " (cutoff:3.500A) Processing sheet with id=AZ7, first strand: chain 'X' and resid 99 through 100 Processing sheet with id=AZ8, first strand: chain 'X' and resid 242 through 246 Processing sheet with id=AZ9, first strand: chain 'X' and resid 242 through 246 removed outlier: 3.576A pdb=" N ALA X 277 " --> pdb=" O GLN X 154 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN X 156 " --> pdb=" O ILE X 275 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE X 275 " --> pdb=" O ASN X 156 " (cutoff:3.500A) Processing sheet with id=BA1, first strand: chain 'X' and resid 179 through 186 removed outlier: 7.050A pdb=" N GLU X 206 " --> pdb=" O THR X 202 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS X 230 " --> pdb=" O GLU X 238 " (cutoff:3.500A) Processing sheet with id=BA2, first strand: chain 'Y' and resid 33 through 35 removed outlier: 4.123A pdb=" N SER Y 33 " --> pdb=" O ASP Y 59 " (cutoff:3.500A) Processing sheet with id=BA3, first strand: chain 'Y' and resid 38 through 39 Processing sheet with id=BA4, first strand: chain 'Y' and resid 65 through 67 Processing sheet with id=BA5, first strand: chain 'Y' and resid 91 through 94 removed outlier: 6.064A pdb=" N ARG Y 83 " --> pdb=" O THR Y 116 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR Y 116 " --> pdb=" O ARG Y 83 " (cutoff:3.500A) Processing sheet with id=BA6, first strand: chain 'Y' and resid 91 through 94 removed outlier: 6.064A pdb=" N ARG Y 83 " --> pdb=" O THR Y 116 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR Y 116 " --> pdb=" O ARG Y 83 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL Y 299 " --> pdb=" O LEU Y 311 " (cutoff:3.500A) Processing sheet with id=BA7, first strand: chain 'Y' and resid 99 through 100 Processing sheet with id=BA8, first strand: chain 'Y' and resid 120 through 121 removed outlier: 3.885A pdb=" N THR Y 126 " --> pdb=" O THR Y 121 " (cutoff:3.500A) Processing sheet with id=BA9, first strand: chain 'Y' and resid 242 through 246 removed outlier: 8.031A pdb=" N MET Y 266 " --> pdb=" O MET Y 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE Y 155 " --> pdb=" O MET Y 266 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN Y 268 " --> pdb=" O ILE Y 155 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU Y 157 " --> pdb=" O GLN Y 268 " (cutoff:3.500A) Processing sheet with id=BB1, first strand: chain 'Y' and resid 242 through 246 removed outlier: 7.491A pdb=" N THR Y 150 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLN Y 280 " --> pdb=" O THR Y 150 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER Y 152 " --> pdb=" O THR Y 278 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR Y 278 " --> pdb=" O SER Y 152 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN Y 154 " --> pdb=" O VAL Y 276 " (cutoff:3.500A) Processing sheet with id=BB2, first strand: chain 'Y' and resid 179 through 186 removed outlier: 7.227A pdb=" N GLU Y 206 " --> pdb=" O THR Y 202 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS Y 230 " --> pdb=" O GLU Y 238 " (cutoff:3.500A) Processing sheet with id=BB3, first strand: chain 'Y' and resid 316 through 318 Processing sheet with id=BB4, first strand: chain 'Y' and resid 326 through 327 removed outlier: 3.510A pdb=" N ALA Y 326 " --> pdb=" O ALA Y 334 " (cutoff:3.500A) Processing sheet with id=BB5, first strand: chain 'Z' and resid 34 through 40 removed outlier: 6.047A pdb=" N THR Z 35 " --> pdb=" O ILE Z 56 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE Z 56 " --> pdb=" O THR Z 35 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER Z 37 " --> pdb=" O ALA Z 54 " (cutoff:3.500A) Processing sheet with id=BB6, first strand: chain 'Z' and resid 65 through 67 Processing sheet with id=BB7, first strand: chain 'Z' and resid 75 through 76 Processing sheet with id=BB8, first strand: chain 'Z' and resid 91 through 94 removed outlier: 5.643A pdb=" N ARG Z 83 " --> pdb=" O THR Z 116 " (cutoff:3.500A) Processing sheet with id=BB9, first strand: chain 'Z' and resid 91 through 94 removed outlier: 5.643A pdb=" N ARG Z 83 " --> pdb=" O THR Z 116 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU Z 308 " --> pdb=" O TYR Z 303 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR Z 303 " --> pdb=" O GLU Z 308 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL Z 310 " --> pdb=" O GLY Z 301 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY Z 301 " --> pdb=" O VAL Z 310 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY Z 312 " --> pdb=" O VAL Z 299 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER Z 290 " --> pdb=" O ASN Z 302 " (cutoff:3.500A) Processing sheet with id=BC1, first strand: chain 'Z' and resid 99 through 100 Processing sheet with id=BC2, first strand: chain 'Z' and resid 120 through 121 removed outlier: 3.824A pdb=" N THR Z 126 " --> pdb=" O THR Z 121 " (cutoff:3.500A) Processing sheet with id=BC3, first strand: chain 'Z' and resid 242 through 246 removed outlier: 7.886A pdb=" N MET Z 266 " --> pdb=" O MET Z 153 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE Z 155 " --> pdb=" O MET Z 266 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN Z 268 " --> pdb=" O ILE Z 155 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU Z 157 " --> pdb=" O GLN Z 268 " (cutoff:3.500A) Processing sheet with id=BC4, first strand: chain 'Z' and resid 242 through 246 removed outlier: 3.798A pdb=" N ALA Z 277 " --> pdb=" O GLN Z 154 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN Z 156 " --> pdb=" O ILE Z 275 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE Z 275 " --> pdb=" O ASN Z 156 " (cutoff:3.500A) Processing sheet with id=BC5, first strand: chain 'Z' and resid 179 through 186 removed outlier: 7.273A pdb=" N LYS Z 230 " --> pdb=" O GLU Z 238 " (cutoff:3.500A) Processing sheet with id=BC6, first strand: chain 'Z' and resid 316 through 318 Processing sheet with id=BC7, first strand: chain 'Z' and resid 326 through 327 3070 hydrogen bonds defined for protein. 8274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 43.15 Time building geometry restraints manager: 25.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 13781 1.28 - 1.41: 18364 1.41 - 1.55: 45312 1.55 - 1.68: 173 1.68 - 1.81: 416 Bond restraints: 78046 Sorted by residual: bond pdb=" C PHE W 81 " pdb=" O PHE W 81 " ideal model delta sigma weight residual 1.235 1.151 0.084 1.25e-02 6.40e+03 4.52e+01 bond pdb=" C ILE W 19 " pdb=" O ILE W 19 " ideal model delta sigma weight residual 1.238 1.153 0.085 1.32e-02 5.74e+03 4.13e+01 bond pdb=" C SER D 3 " pdb=" O SER D 3 " ideal model delta sigma weight residual 1.236 1.167 0.068 1.18e-02 7.18e+03 3.37e+01 bond pdb=" CA THR S 387 " pdb=" C THR S 387 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.39e-02 5.18e+03 3.18e+01 bond pdb=" CA TYR U 93 " pdb=" C TYR U 93 " ideal model delta sigma weight residual 1.520 1.455 0.066 1.22e-02 6.72e+03 2.91e+01 ... (remaining 78041 not shown) Histogram of bond angle deviations from ideal: 95.14 - 103.59: 834 103.59 - 112.05: 36703 112.05 - 120.50: 36868 120.50 - 128.95: 31673 128.95 - 137.40: 254 Bond angle restraints: 106332 Sorted by residual: angle pdb=" C VAL G 74 " pdb=" CA VAL G 74 " pdb=" CB VAL G 74 " ideal model delta sigma weight residual 111.59 98.47 13.12 1.10e+00 8.26e-01 1.42e+02 angle pdb=" N GLY W 80 " pdb=" CA GLY W 80 " pdb=" C GLY W 80 " ideal model delta sigma weight residual 112.25 122.45 -10.20 1.34e+00 5.57e-01 5.79e+01 angle pdb=" N GLY W 20 " pdb=" CA GLY W 20 " pdb=" C GLY W 20 " ideal model delta sigma weight residual 112.49 104.47 8.02 1.21e+00 6.83e-01 4.39e+01 angle pdb=" C VAL U 332 " pdb=" CA VAL U 332 " pdb=" CB VAL U 332 " ideal model delta sigma weight residual 111.29 100.52 10.77 1.64e+00 3.72e-01 4.31e+01 angle pdb=" C SER A 77 " pdb=" N GLN A 78 " pdb=" CA GLN A 78 " ideal model delta sigma weight residual 121.54 132.49 -10.95 1.91e+00 2.74e-01 3.29e+01 ... (remaining 106327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 43568 16.84 - 33.68: 2097 33.68 - 50.52: 382 50.52 - 67.36: 49 67.36 - 84.19: 76 Dihedral angle restraints: 46172 sinusoidal: 16587 harmonic: 29585 Sorted by residual: dihedral pdb=" CA LYS A 284 " pdb=" C LYS A 284 " pdb=" N PRO A 285 " pdb=" CA PRO A 285 " ideal model delta harmonic sigma weight residual 180.00 123.47 56.53 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA SER Z 77 " pdb=" C SER Z 77 " pdb=" N GLN Z 78 " pdb=" CA GLN Z 78 " ideal model delta harmonic sigma weight residual 180.00 145.23 34.77 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" CA GLN Y 268 " pdb=" C GLN Y 268 " pdb=" N ASN Y 269 " pdb=" CA ASN Y 269 " ideal model delta harmonic sigma weight residual 180.00 -148.97 -31.03 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 46169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 11320 0.102 - 0.205: 1051 0.205 - 0.307: 89 0.307 - 0.410: 11 0.410 - 0.512: 8 Chirality restraints: 12479 Sorted by residual: chirality pdb=" CA ASN W 79 " pdb=" N ASN W 79 " pdb=" C ASN W 79 " pdb=" CB ASN W 79 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CB ILE N 388 " pdb=" CA ILE N 388 " pdb=" CG1 ILE N 388 " pdb=" CG2 ILE N 388 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CB ILE F 388 " pdb=" CA ILE F 388 " pdb=" CG1 ILE F 388 " pdb=" CG2 ILE F 388 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.33e+00 ... (remaining 12476 not shown) Planarity restraints: 14273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 284 " 0.084 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO A 285 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY U 329 " -0.022 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C GLY U 329 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY U 329 " -0.031 2.00e-02 2.50e+03 pdb=" N ASP U 330 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 10 " -0.021 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C ASN E 10 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN E 10 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA E 11 " -0.024 2.00e-02 2.50e+03 ... (remaining 14270 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 12 2.22 - 2.89: 31791 2.89 - 3.56: 111513 3.56 - 4.23: 187194 4.23 - 4.90: 312787 Nonbonded interactions: 643297 Sorted by model distance: nonbonded pdb=" OD1 ASP V 73 " pdb=" CG LEU V 360 " model vdw 1.554 3.470 nonbonded pdb=" OD1 ASN W 21 " pdb=" OD1 ASN W 25 " model vdw 1.949 3.040 nonbonded pdb=" OD1 ASP V 73 " pdb=" CD2 LEU V 360 " model vdw 1.995 3.460 nonbonded pdb=" O ASN S 380 " pdb=" OG SER S 383 " model vdw 2.072 2.440 nonbonded pdb=" O ASN F 25 " pdb=" OD1 ASN F 25 " model vdw 2.123 3.040 ... (remaining 643292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 402) selection = (chain 'B' and resid 2 through 402) selection = (chain 'C' and resid 2 through 402) selection = (chain 'D' and resid 2 through 402) selection = (chain 'E' and resid 2 through 402) selection = (chain 'F' and resid 2 through 402) selection = (chain 'G' and resid 2 through 402) selection = (chain 'H' and resid 2 through 402) selection = (chain 'I' and resid 2 through 402) selection = (chain 'J' and resid 2 through 402) selection = (chain 'K' and resid 2 through 402) selection = (chain 'L' and resid 2 through 402) selection = (chain 'M' and resid 2 through 402) selection = (chain 'N' and resid 2 through 402) selection = (chain 'O' and resid 2 through 402) selection = (chain 'P' and resid 2 through 402) selection = chain 'Q' selection = (chain 'R' and resid 2 through 402) selection = (chain 'S' and resid 2 through 402) selection = (chain 'T' and resid 2 through 402) selection = (chain 'U' and resid 2 through 402) selection = (chain 'V' and resid 2 through 402) selection = (chain 'W' and resid 2 through 402) selection = (chain 'X' and resid 2 through 402) selection = (chain 'Y' and resid 2 through 402) selection = (chain 'Z' and resid 2 through 402) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 10.520 Check model and map are aligned: 0.870 Set scattering table: 0.560 Process input model: 174.650 Find NCS groups from input model: 5.050 Set up NCS constraints: 0.320 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: 0.030 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 78046 Z= 0.453 Angle : 1.086 15.557 106332 Z= 0.607 Chirality : 0.064 0.512 12479 Planarity : 0.007 0.129 14273 Dihedral : 11.348 84.195 27298 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 0.29 % Allowed : 5.22 % Favored : 94.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.02 % 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: -3.33 (0.07), residues: 10399 helix: -2.10 (0.10), residues: 1510 sheet: -2.20 (0.08), residues: 2996 loop : -2.26 (0.07), residues: 5893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP S 333 HIS 0.008 0.002 HIS N 212 PHE 0.034 0.004 PHE U 352 TYR 0.049 0.004 TYR B 93 ARG 0.015 0.001 ARG P 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1970 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1946 time to evaluate : 6.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 THR cc_start: 0.8620 (p) cc_final: 0.8128 (p) REVERT: B 173 ASP cc_start: 0.7165 (t0) cc_final: 0.6953 (t0) REVERT: B 283 TYR cc_start: 0.7000 (p90) cc_final: 0.5955 (p90) REVERT: B 389 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6050 (mttm) REVERT: C 105 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.5873 (mtt-85) REVERT: C 194 ASP cc_start: 0.8151 (p0) cc_final: 0.7885 (p0) REVERT: C 259 SER cc_start: 0.8096 (t) cc_final: 0.7827 (p) REVERT: D 172 SER cc_start: 0.8986 (m) cc_final: 0.8694 (p) REVERT: E 233 GLU cc_start: 0.5281 (tt0) cc_final: 0.4371 (tp30) REVERT: F 40 ASP cc_start: 0.7726 (p0) cc_final: 0.7500 (p0) REVERT: F 280 GLN cc_start: 0.8236 (pp30) cc_final: 0.7822 (pp30) REVERT: G 40 ASP cc_start: 0.7650 (m-30) cc_final: 0.7184 (m-30) REVERT: H 210 TYR cc_start: 0.7433 (m-80) cc_final: 0.7135 (m-80) REVERT: H 308 GLU cc_start: 0.7071 (mp0) cc_final: 0.6672 (mm-30) REVERT: H 379 ARG cc_start: 0.8337 (mmt-90) cc_final: 0.7869 (mmt180) REVERT: I 195 MET cc_start: 0.7895 (mmm) cc_final: 0.7664 (mmm) REVERT: I 303 TYR cc_start: 0.7003 (m-80) cc_final: 0.6777 (m-80) REVERT: I 381 TYR cc_start: 0.8263 (t80) cc_final: 0.7951 (t80) REVERT: J 274 ASN cc_start: 0.7458 (t0) cc_final: 0.7185 (t0) REVERT: K 167 THR cc_start: 0.6743 (m) cc_final: 0.6216 (p) REVERT: L 361 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7450 (tm-30) REVERT: M 68 THR cc_start: 0.8281 (m) cc_final: 0.7915 (p) REVERT: M 283 TYR cc_start: 0.7527 (p90) cc_final: 0.7293 (p90) REVERT: N 17 ASP cc_start: 0.7547 (t0) cc_final: 0.7307 (t0) REVERT: N 210 TYR cc_start: 0.8001 (m-10) cc_final: 0.7659 (m-80) REVERT: O 41 MET cc_start: 0.8278 (mpp) cc_final: 0.7711 (mpp) REVERT: O 291 TYR cc_start: 0.7257 (p90) cc_final: 0.7028 (p90) REVERT: P 373 ASN cc_start: 0.8072 (t0) cc_final: 0.7838 (t0) REVERT: Q 57 THR cc_start: 0.7919 (m) cc_final: 0.7697 (m) REVERT: R 23 ILE cc_start: 0.8797 (mt) cc_final: 0.8455 (mt) REVERT: S 230 LYS cc_start: 0.8072 (tptp) cc_final: 0.7658 (tptt) REVERT: T 210 TYR cc_start: 0.8463 (m-10) cc_final: 0.7897 (m-80) REVERT: T 266 MET cc_start: 0.6989 (mtp) cc_final: 0.6488 (ttt) REVERT: U 41 MET cc_start: 0.7644 (mpt) cc_final: 0.7143 (mpt) REVERT: U 223 THR cc_start: 0.7286 (m) cc_final: 0.6911 (p) REVERT: U 367 LEU cc_start: 0.8337 (tt) cc_final: 0.8022 (tp) REVERT: V 380 ASN cc_start: 0.8652 (p0) cc_final: 0.8357 (p0) REVERT: W 46 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.4744 (pttt) REVERT: W 393 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7417 (tm-30) REVERT: X 67 ASN cc_start: 0.8491 (m-40) cc_final: 0.8153 (t0) REVERT: X 79 ASN cc_start: 0.7027 (t0) cc_final: 0.6597 (t0) REVERT: X 95 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.7225 (mmm160) REVERT: X 263 LEU cc_start: 0.8113 (mt) cc_final: 0.7879 (mp) REVERT: X 303 TYR cc_start: 0.7403 (m-10) cc_final: 0.7029 (m-10) REVERT: X 341 VAL cc_start: 0.8221 (t) cc_final: 0.7959 (m) REVERT: Y 19 ILE cc_start: 0.8787 (pt) cc_final: 0.8266 (mm) REVERT: Y 375 ILE cc_start: 0.8545 (pt) cc_final: 0.7844 (pt) REVERT: Z 234 ASN cc_start: 0.7912 (p0) cc_final: 0.7422 (p0) REVERT: Z 381 TYR cc_start: 0.8279 (t80) cc_final: 0.7890 (t80) REVERT: Z 389 LYS cc_start: 0.8345 (tttm) cc_final: 0.8143 (tttt) outliers start: 24 outliers final: 14 residues processed: 1964 average time/residue: 0.7449 time to fit residues: 2548.5609 Evaluate side-chains 1284 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1269 time to evaluate : 6.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain X residue 299 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 878 optimal weight: 3.9990 chunk 788 optimal weight: 5.9990 chunk 437 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 531 optimal weight: 8.9990 chunk 421 optimal weight: 7.9990 chunk 815 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 chunk 495 optimal weight: 3.9990 chunk 606 optimal weight: 0.9980 chunk 944 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 264 ASN A 294 ASN A 313 GLN B 79 ASN B 302 ASN B 393 GLN B 400 ASN C 132 ASN C 295 ASN C 309 GLN C 393 GLN D 98 GLN ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 ASN F 393 GLN F 396 ASN G 10 ASN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN G 337 GLN G 386 GLN G 400 ASN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 ASN H 193 HIS H 391 GLN ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 ASN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 205 ASN J 98 GLN K 302 ASN K 351 ASN K 391 GLN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 328 GLN L 400 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 ASN M 193 HIS ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 331 ASN ** M 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 58 GLN N 156 ASN N 267 GLN N 322 ASN N 331 ASN N 373 ASN O 267 GLN O 400 ASN P 328 GLN Q 4 GLN ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 ASN R 373 ASN S 67 ASN S 79 ASN S 114 GLN ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 295 ASN S 337 GLN S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 302 ASN T 321 ASN U 292 GLN U 302 ASN ** U 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 307 GLN ** V 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 400 ASN ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 128 GLN ** W 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 281 ASN W 309 GLN W 382 GLN W 391 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 156 ASN ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN X 351 ASN X 373 ASN Y 264 ASN Y 267 GLN Y 331 ASN Y 357 ASN ** Y 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 386 GLN Y 393 GLN Z 25 ASN Z 140 ASN Z 307 GLN ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 78046 Z= 0.228 Angle : 0.663 13.554 106332 Z= 0.358 Chirality : 0.044 0.274 12479 Planarity : 0.004 0.109 14273 Dihedral : 6.275 54.667 10889 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.32 % Favored : 94.66 % Rotamer: Outliers : 2.99 % Allowed : 11.17 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -2.41 (0.07), residues: 10399 helix: -0.19 (0.12), residues: 1508 sheet: -1.97 (0.09), residues: 2893 loop : -1.79 (0.07), residues: 5998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 333 HIS 0.011 0.001 HIS H 193 PHE 0.017 0.002 PHE T 199 TYR 0.023 0.002 TYR J 381 ARG 0.009 0.001 ARG L 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1660 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1410 time to evaluate : 6.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7887 (mm-40) cc_final: 0.6982 (mm-40) REVERT: A 179 LYS cc_start: 0.7924 (tptp) cc_final: 0.7675 (tptp) REVERT: A 186 TYR cc_start: 0.7497 (m-10) cc_final: 0.7295 (m-10) REVERT: B 283 TYR cc_start: 0.7104 (p90) cc_final: 0.6188 (p90) REVERT: B 389 LYS cc_start: 0.6986 (mmtt) cc_final: 0.6304 (mttm) REVERT: C 105 ARG cc_start: 0.8099 (mtp-110) cc_final: 0.6169 (mmt180) REVERT: C 194 ASP cc_start: 0.8314 (p0) cc_final: 0.8046 (p0) REVERT: C 308 GLU cc_start: 0.8133 (pm20) cc_final: 0.7792 (pp20) REVERT: D 172 SER cc_start: 0.8951 (m) cc_final: 0.8692 (p) REVERT: E 233 GLU cc_start: 0.5419 (tt0) cc_final: 0.4474 (tp30) REVERT: F 40 ASP cc_start: 0.7450 (p0) cc_final: 0.7220 (p0) REVERT: F 49 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8177 (mt) REVERT: F 51 VAL cc_start: 0.8790 (p) cc_final: 0.8546 (t) REVERT: F 280 GLN cc_start: 0.8257 (pp30) cc_final: 0.7851 (pp30) REVERT: F 323 GLU cc_start: 0.7826 (pp20) cc_final: 0.7604 (pp20) REVERT: G 287 ASP cc_start: 0.5937 (p0) cc_final: 0.5674 (p0) REVERT: H 155 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8080 (tp) REVERT: H 156 ASN cc_start: 0.7874 (p0) cc_final: 0.7116 (p0) REVERT: H 379 ARG cc_start: 0.8403 (mmt-90) cc_final: 0.8004 (mmt180) REVERT: I 199 PHE cc_start: 0.7457 (m-80) cc_final: 0.7232 (m-10) REVERT: I 270 THR cc_start: 0.5870 (OUTLIER) cc_final: 0.5420 (p) REVERT: J 274 ASN cc_start: 0.7591 (t0) cc_final: 0.7311 (t0) REVERT: L 113 MET cc_start: 0.7112 (ttm) cc_final: 0.6774 (ttm) REVERT: L 238 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7028 (mm-30) REVERT: L 364 ASN cc_start: 0.7688 (t0) cc_final: 0.6546 (t0) REVERT: M 68 THR cc_start: 0.8261 (m) cc_final: 0.7783 (p) REVERT: M 113 MET cc_start: 0.7720 (mtp) cc_final: 0.7463 (ptp) REVERT: M 153 MET cc_start: 0.7213 (ttt) cc_final: 0.6938 (ttt) REVERT: N 210 TYR cc_start: 0.7747 (m-10) cc_final: 0.7473 (m-80) REVERT: N 402 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7273 (ttp80) REVERT: O 41 MET cc_start: 0.8394 (mpp) cc_final: 0.7784 (mpp) REVERT: O 73 ASP cc_start: 0.6919 (p0) cc_final: 0.6554 (p0) REVERT: O 291 TYR cc_start: 0.7407 (p90) cc_final: 0.7159 (p90) REVERT: P 19 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8159 (mm) REVERT: P 373 ASN cc_start: 0.7960 (t0) cc_final: 0.7738 (t0) REVERT: Q 67 ASN cc_start: 0.8392 (m-40) cc_final: 0.7763 (m-40) REVERT: Q 283 TYR cc_start: 0.8371 (p90) cc_final: 0.7960 (p90) REVERT: Q 398 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8643 (pt) REVERT: R 195 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8525 (mmt) REVERT: R 356 THR cc_start: 0.8351 (t) cc_final: 0.8131 (m) REVERT: S 233 GLU cc_start: 0.8435 (mp0) cc_final: 0.8117 (mp0) REVERT: T 210 TYR cc_start: 0.8470 (m-10) cc_final: 0.8087 (m-80) REVERT: T 266 MET cc_start: 0.7083 (mtp) cc_final: 0.6644 (ttt) REVERT: T 273 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6709 (p0) REVERT: U 41 MET cc_start: 0.7534 (mpt) cc_final: 0.6928 (mpt) REVERT: U 73 ASP cc_start: 0.7146 (t0) cc_final: 0.6839 (t0) REVERT: U 223 THR cc_start: 0.7192 (m) cc_final: 0.6919 (p) REVERT: U 308 GLU cc_start: 0.7374 (mp0) cc_final: 0.6755 (mp0) REVERT: U 389 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8620 (ttpp) REVERT: V 110 MET cc_start: 0.8163 (mpp) cc_final: 0.7882 (mmm) REVERT: V 113 MET cc_start: 0.8002 (mpp) cc_final: 0.7538 (mtm) REVERT: V 136 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8880 (mp) REVERT: W 46 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.4997 (ptmt) REVERT: W 393 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7539 (tm-30) REVERT: X 79 ASN cc_start: 0.6961 (t0) cc_final: 0.6534 (t0) REVERT: X 341 VAL cc_start: 0.8112 (t) cc_final: 0.7883 (m) REVERT: X 354 LYS cc_start: 0.5982 (mmpt) cc_final: 0.5748 (mttt) REVERT: X 361 GLU cc_start: 0.8158 (tt0) cc_final: 0.7878 (tt0) REVERT: X 386 GLN cc_start: 0.7646 (tp40) cc_final: 0.7241 (tp-100) REVERT: Y 378 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7028 (tm-30) REVERT: Y 391 GLN cc_start: 0.8073 (mp10) cc_final: 0.7869 (mp10) REVERT: Z 381 TYR cc_start: 0.8399 (t80) cc_final: 0.8010 (t80) REVERT: Z 389 LYS cc_start: 0.8426 (tttm) cc_final: 0.8111 (tttt) outliers start: 250 outliers final: 153 residues processed: 1564 average time/residue: 0.6655 time to fit residues: 1825.3835 Evaluate side-chains 1367 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1205 time to evaluate : 6.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 357 ASN Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 58 GLN Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 331 ASN Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 308 GLU Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain Q residue 398 LEU Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 79 ASN Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 273 ASN Chi-restraints excluded: chain T residue 321 ASN Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 ILE Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 391 GLN Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 137 THR Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 61 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 264 ASN Chi-restraints excluded: chain Y residue 383 SER Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 393 GLN Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 278 THR Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 524 optimal weight: 20.0000 chunk 293 optimal weight: 6.9990 chunk 786 optimal weight: 20.0000 chunk 643 optimal weight: 9.9990 chunk 260 optimal weight: 30.0000 chunk 946 optimal weight: 20.0000 chunk 1022 optimal weight: 8.9990 chunk 842 optimal weight: 3.9990 chunk 938 optimal weight: 20.0000 chunk 322 optimal weight: 9.9990 chunk 759 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 264 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 309 GLN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN D 393 GLN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 ASN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 318 ASN G 382 GLN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 318 ASN H 357 ASN ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN I 357 ASN ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 GLN K 196 ASN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN L 322 ASN L 357 ASN L 364 ASN L 400 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN N 331 ASN ** N 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 ASN P 67 ASN ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 373 ASN ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** V 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 268 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN Y 268 GLN ** Y 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 380 ASN Y 384 ASN Y 393 GLN Z 140 ASN Z 205 ASN Z 307 GLN Z 309 GLN ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 391 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 78046 Z= 0.358 Angle : 0.689 10.283 106332 Z= 0.373 Chirality : 0.045 0.280 12479 Planarity : 0.004 0.110 14273 Dihedral : 6.083 59.849 10884 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.12 % Favored : 93.86 % Rotamer: Outliers : 4.46 % Allowed : 13.27 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -2.08 (0.08), residues: 10399 helix: 0.44 (0.13), residues: 1516 sheet: -1.89 (0.09), residues: 2772 loop : -1.62 (0.07), residues: 6111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Z 333 HIS 0.005 0.001 HIS T 212 PHE 0.034 0.002 PHE U 352 TYR 0.023 0.002 TYR J 381 ARG 0.009 0.001 ARG S 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1651 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 1278 time to evaluate : 6.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7702 (mm-40) cc_final: 0.6526 (tp40) REVERT: A 186 TYR cc_start: 0.7647 (m-10) cc_final: 0.7418 (m-10) REVERT: B 70 ARG cc_start: 0.7988 (tmm-80) cc_final: 0.7417 (ttp80) REVERT: B 95 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7366 (mtp180) REVERT: B 283 TYR cc_start: 0.7327 (p90) cc_final: 0.6186 (p90) REVERT: B 389 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6499 (mttm) REVERT: C 113 MET cc_start: 0.7563 (mmt) cc_final: 0.7170 (mmt) REVERT: C 194 ASP cc_start: 0.8414 (p0) cc_final: 0.8161 (p0) REVERT: C 308 GLU cc_start: 0.8268 (pm20) cc_final: 0.7965 (pp20) REVERT: D 172 SER cc_start: 0.8956 (m) cc_final: 0.8701 (p) REVERT: D 379 ARG cc_start: 0.5471 (mtt180) cc_final: 0.4926 (mtt180) REVERT: D 398 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8601 (tt) REVERT: E 49 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8742 (pp) REVERT: E 233 GLU cc_start: 0.5531 (tt0) cc_final: 0.4484 (tp30) REVERT: G 100 LYS cc_start: 0.7923 (pttt) cc_final: 0.7585 (pttt) REVERT: G 287 ASP cc_start: 0.6134 (p0) cc_final: 0.5683 (p0) REVERT: H 155 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8175 (tp) REVERT: H 156 ASN cc_start: 0.7996 (p0) cc_final: 0.7374 (p0) REVERT: H 177 TYR cc_start: 0.8239 (p90) cc_final: 0.7938 (p90) REVERT: I 41 MET cc_start: 0.7896 (mpp) cc_final: 0.7568 (mtp) REVERT: I 199 PHE cc_start: 0.7485 (m-80) cc_final: 0.7280 (m-10) REVERT: I 270 THR cc_start: 0.6032 (OUTLIER) cc_final: 0.5719 (p) REVERT: I 373 ASN cc_start: 0.8102 (t0) cc_final: 0.7791 (t0) REVERT: J 274 ASN cc_start: 0.7586 (t0) cc_final: 0.7353 (t0) REVERT: K 78 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6772 (tp-100) REVERT: K 318 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7315 (m110) REVERT: M 113 MET cc_start: 0.7880 (mtp) cc_final: 0.7552 (ptp) REVERT: M 153 MET cc_start: 0.7200 (ttt) cc_final: 0.6936 (ttt) REVERT: M 343 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7686 (mm) REVERT: N 41 MET cc_start: 0.8766 (mpt) cc_final: 0.8143 (mpt) REVERT: N 113 MET cc_start: 0.8387 (mmp) cc_final: 0.7797 (mmp) REVERT: N 136 ILE cc_start: 0.8449 (pp) cc_final: 0.8244 (pt) REVERT: N 210 TYR cc_start: 0.7769 (m-10) cc_final: 0.7404 (m-80) REVERT: O 41 MET cc_start: 0.8486 (mpp) cc_final: 0.7663 (mpp) REVERT: O 73 ASP cc_start: 0.7040 (p0) cc_final: 0.6664 (p0) REVERT: O 78 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7429 (mm-40) REVERT: O 291 TYR cc_start: 0.7517 (p90) cc_final: 0.7287 (p90) REVERT: P 373 ASN cc_start: 0.8163 (t0) cc_final: 0.7864 (t0) REVERT: Q 283 TYR cc_start: 0.8488 (p90) cc_final: 0.7992 (p90) REVERT: Q 296 ASP cc_start: 0.7503 (p0) cc_final: 0.7158 (p0) REVERT: R 78 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: R 113 MET cc_start: 0.8501 (mmm) cc_final: 0.7705 (mmm) REVERT: S 233 GLU cc_start: 0.8336 (mp0) cc_final: 0.8026 (mp0) REVERT: T 118 TYR cc_start: 0.8042 (m-10) cc_final: 0.7813 (m-10) REVERT: T 153 MET cc_start: 0.7864 (mtt) cc_final: 0.7447 (ttm) REVERT: T 195 MET cc_start: 0.6962 (mmm) cc_final: 0.6734 (mmm) REVERT: T 210 TYR cc_start: 0.8495 (m-10) cc_final: 0.8170 (m-80) REVERT: T 266 MET cc_start: 0.7055 (mtp) cc_final: 0.6484 (ttt) REVERT: U 41 MET cc_start: 0.7490 (mpt) cc_final: 0.6901 (mpt) REVERT: U 73 ASP cc_start: 0.7188 (t0) cc_final: 0.6586 (t0) REVERT: U 308 GLU cc_start: 0.7448 (mp0) cc_final: 0.6996 (mp0) REVERT: V 17 ASP cc_start: 0.7706 (m-30) cc_final: 0.7503 (m-30) REVERT: V 81 PHE cc_start: 0.8453 (m-80) cc_final: 0.7747 (m-10) REVERT: V 136 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8950 (mp) REVERT: W 233 GLU cc_start: 0.7952 (mp0) cc_final: 0.7736 (mp0) REVERT: W 366 ASP cc_start: 0.7536 (p0) cc_final: 0.6995 (p0) REVERT: W 369 LYS cc_start: 0.7838 (ttpm) cc_final: 0.7514 (pttm) REVERT: X 79 ASN cc_start: 0.6842 (t0) cc_final: 0.6395 (t0) REVERT: X 153 MET cc_start: 0.7500 (ttt) cc_final: 0.7259 (ttt) REVERT: X 291 TYR cc_start: 0.8080 (p90) cc_final: 0.7853 (p90) REVERT: X 303 TYR cc_start: 0.7848 (m-10) cc_final: 0.7626 (m-10) REVERT: X 354 LYS cc_start: 0.5998 (mmpt) cc_final: 0.5676 (mttt) REVERT: X 386 GLN cc_start: 0.7581 (tp40) cc_final: 0.7245 (tp-100) REVERT: Y 391 GLN cc_start: 0.8048 (mp10) cc_final: 0.7255 (mp10) REVERT: Z 381 TYR cc_start: 0.8429 (t80) cc_final: 0.7839 (t80) REVERT: Z 382 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7076 (mt0) REVERT: Z 389 LYS cc_start: 0.8368 (tttm) cc_final: 0.8077 (tttm) outliers start: 373 outliers final: 252 residues processed: 1521 average time/residue: 0.6731 time to fit residues: 1801.2212 Evaluate side-chains 1449 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1186 time to evaluate : 6.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 382 GLN Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ASN Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 388 ILE Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 322 ASN Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain K residue 396 ASN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 293 ILE Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 322 ASN Chi-restraints excluded: chain L residue 337 GLN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 332 VAL Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 383 SER Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 289 VAL Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 332 VAL Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 257 THR Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 346 THR Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 375 ILE Chi-restraints excluded: chain Q residue 388 ILE Chi-restraints excluded: chain Q residue 395 LEU Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 79 ASN Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 143 MET Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 302 ASN Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 382 GLN Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 136 ILE Chi-restraints excluded: chain V residue 138 ILE Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain W residue 365 VAL Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 137 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 368 SER Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 61 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 110 MET Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 383 SER Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 278 THR Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 366 ASP Chi-restraints excluded: chain Z residue 382 GLN Chi-restraints excluded: chain Z residue 387 THR Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 934 optimal weight: 0.1980 chunk 711 optimal weight: 6.9990 chunk 491 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 451 optimal weight: 6.9990 chunk 635 optimal weight: 1.9990 chunk 949 optimal weight: 9.9990 chunk 1005 optimal weight: 10.0000 chunk 496 optimal weight: 0.0970 chunk 899 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 364 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN D 96 ASN E 25 ASN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN F 351 ASN F 393 GLN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 382 GLN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 269 ASN ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN I 386 GLN ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 373 ASN J 393 GLN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 322 ASN L 400 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN N 386 GLN ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN P 268 GLN ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 GLN ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN ** S 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 337 GLN S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 321 ASN T 393 GLN ** V 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 ASN W 391 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 196 ASN ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 GLN X 321 ASN X 400 ASN Y 268 GLN Y 357 ASN Y 393 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 140 ASN Z 156 ASN ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 78046 Z= 0.182 Angle : 0.602 10.562 106332 Z= 0.321 Chirality : 0.043 0.261 12479 Planarity : 0.004 0.106 14273 Dihedral : 5.522 54.870 10880 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.95 % Rotamer: Outliers : 3.93 % Allowed : 15.26 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.71 (0.08), residues: 10399 helix: 1.01 (0.13), residues: 1523 sheet: -1.68 (0.09), residues: 2708 loop : -1.44 (0.07), residues: 6168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 333 HIS 0.003 0.001 HIS V 212 PHE 0.022 0.001 PHE N 42 TYR 0.019 0.002 TYR M 283 ARG 0.010 0.001 ARG S 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1682 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1353 time to evaluate : 6.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7518 (mm-40) cc_final: 0.6477 (tp40) REVERT: A 186 TYR cc_start: 0.7606 (m-10) cc_final: 0.7393 (m-10) REVERT: A 195 MET cc_start: 0.7758 (mmm) cc_final: 0.7529 (mmm) REVERT: B 70 ARG cc_start: 0.7840 (tmm-80) cc_final: 0.7638 (ptm-80) REVERT: B 95 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7423 (mtt90) REVERT: B 184 THR cc_start: 0.8886 (m) cc_final: 0.8396 (p) REVERT: B 283 TYR cc_start: 0.7154 (p90) cc_final: 0.6323 (p90) REVERT: B 389 LYS cc_start: 0.6929 (mmtt) cc_final: 0.6342 (mttm) REVERT: C 113 MET cc_start: 0.7465 (mmt) cc_final: 0.7135 (mmt) REVERT: C 194 ASP cc_start: 0.8362 (p0) cc_final: 0.8068 (p0) REVERT: D 17 ASP cc_start: 0.6977 (t0) cc_final: 0.6629 (t0) REVERT: D 172 SER cc_start: 0.8936 (m) cc_final: 0.8676 (p) REVERT: D 379 ARG cc_start: 0.5380 (mtt180) cc_final: 0.4914 (mtt180) REVERT: E 49 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8724 (pp) REVERT: E 233 GLU cc_start: 0.5421 (tt0) cc_final: 0.4453 (tp30) REVERT: F 9 LEU cc_start: 0.8187 (mt) cc_final: 0.7897 (mp) REVERT: F 275 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8779 (pt) REVERT: G 100 LYS cc_start: 0.7876 (pttt) cc_final: 0.7630 (pttm) REVERT: G 110 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6936 (mtp) REVERT: G 287 ASP cc_start: 0.6075 (p0) cc_final: 0.5521 (p0) REVERT: H 155 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8171 (tp) REVERT: H 156 ASN cc_start: 0.8009 (p0) cc_final: 0.7341 (p0) REVERT: H 177 TYR cc_start: 0.8309 (p90) cc_final: 0.7960 (p90) REVERT: I 41 MET cc_start: 0.7771 (mpp) cc_final: 0.7465 (mtp) REVERT: I 270 THR cc_start: 0.5729 (OUTLIER) cc_final: 0.5459 (p) REVERT: I 373 ASN cc_start: 0.8200 (t0) cc_final: 0.7876 (t0) REVERT: I 395 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8350 (mp) REVERT: J 49 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8243 (mt) REVERT: J 274 ASN cc_start: 0.7791 (t0) cc_final: 0.7532 (t0) REVERT: K 78 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6522 (tp-100) REVERT: K 318 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7301 (m-40) REVERT: L 70 ARG cc_start: 0.7161 (tmm-80) cc_final: 0.6916 (ttt-90) REVERT: L 238 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7089 (mm-30) REVERT: L 366 ASP cc_start: 0.6755 (p0) cc_final: 0.6529 (p0) REVERT: L 400 ASN cc_start: 0.8493 (m-40) cc_final: 0.8166 (m110) REVERT: M 153 MET cc_start: 0.7270 (ttt) cc_final: 0.7006 (ttt) REVERT: M 266 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6024 (ttt) REVERT: M 343 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7632 (mm) REVERT: N 41 MET cc_start: 0.8726 (mpt) cc_final: 0.8219 (mpt) REVERT: N 210 TYR cc_start: 0.7713 (m-10) cc_final: 0.7219 (m-80) REVERT: O 40 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7596 (p0) REVERT: O 73 ASP cc_start: 0.6895 (p0) cc_final: 0.6600 (p0) REVERT: O 291 TYR cc_start: 0.7454 (p90) cc_final: 0.7218 (p90) REVERT: O 357 ASN cc_start: 0.6776 (OUTLIER) cc_final: 0.6348 (m-40) REVERT: P 366 ASP cc_start: 0.8182 (p0) cc_final: 0.7953 (p0) REVERT: P 373 ASN cc_start: 0.7964 (t0) cc_final: 0.7620 (t0) REVERT: Q 283 TYR cc_start: 0.8367 (p90) cc_final: 0.7854 (p90) REVERT: Q 296 ASP cc_start: 0.7364 (p0) cc_final: 0.7020 (p0) REVERT: R 113 MET cc_start: 0.8394 (mmm) cc_final: 0.7637 (mmm) REVERT: S 143 MET cc_start: 0.7753 (tpt) cc_final: 0.7495 (tpt) REVERT: S 233 GLU cc_start: 0.8296 (mp0) cc_final: 0.8039 (mp0) REVERT: T 46 LYS cc_start: 0.7066 (mtmm) cc_final: 0.6832 (mtpt) REVERT: T 153 MET cc_start: 0.7959 (mtt) cc_final: 0.7470 (ttm) REVERT: T 210 TYR cc_start: 0.8476 (m-10) cc_final: 0.8178 (m-80) REVERT: T 266 MET cc_start: 0.7079 (mtp) cc_final: 0.6542 (ttt) REVERT: T 273 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6720 (p0) REVERT: U 41 MET cc_start: 0.7596 (mpt) cc_final: 0.6959 (mpt) REVERT: U 223 THR cc_start: 0.7296 (m) cc_final: 0.6989 (p) REVERT: U 308 GLU cc_start: 0.7349 (mp0) cc_final: 0.7000 (mp0) REVERT: V 110 MET cc_start: 0.8256 (mpp) cc_final: 0.7966 (mmm) REVERT: W 352 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5851 (t80) REVERT: X 303 TYR cc_start: 0.7709 (m-10) cc_final: 0.7495 (m-10) REVERT: X 313 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8346 (mp10) REVERT: X 354 LYS cc_start: 0.6170 (mmpt) cc_final: 0.5835 (mttt) REVERT: X 386 GLN cc_start: 0.7460 (tp40) cc_final: 0.7137 (tp-100) REVERT: Y 391 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: Z 370 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7150 (mm-30) REVERT: Z 381 TYR cc_start: 0.8406 (t80) cc_final: 0.7797 (t80) REVERT: Z 382 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: Z 389 LYS cc_start: 0.8342 (tttm) cc_final: 0.8027 (tttm) outliers start: 329 outliers final: 202 residues processed: 1569 average time/residue: 0.7037 time to fit residues: 1961.3716 Evaluate side-chains 1418 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1197 time to evaluate : 6.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 318 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ASN Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 306 GLU Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 279 ASN Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 393 GLN Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 70 ARG Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 266 MET Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 40 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 357 ASN Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 332 VAL Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 308 GLU Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 307 GLN Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 276 VAL Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain S residue 387 THR Chi-restraints excluded: chain S residue 388 ILE Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 79 ASN Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 273 ASN Chi-restraints excluded: chain T residue 321 ASN Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain T residue 393 GLN Chi-restraints excluded: chain T residue 395 LEU Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 302 ASN Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain W residue 236 ILE Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain W residue 391 GLN Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 263 LEU Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 313 GLN Chi-restraints excluded: chain X residue 332 VAL Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 376 VAL Chi-restraints excluded: chain X residue 394 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 110 MET Chi-restraints excluded: chain Y residue 183 VAL Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 391 GLN Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 366 ASP Chi-restraints excluded: chain Z residue 382 GLN Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 837 optimal weight: 6.9990 chunk 570 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 748 optimal weight: 7.9990 chunk 414 optimal weight: 6.9990 chunk 857 optimal weight: 8.9990 chunk 694 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 513 optimal weight: 8.9990 chunk 902 optimal weight: 0.3980 chunk 253 optimal weight: 0.4980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 364 ASN A 400 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN D 4 GLN E 25 ASN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 GLN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 GLN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 364 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN ** N 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN O 391 GLN P 67 ASN P 268 GLN P 279 ASN ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 331 ASN Q 364 ASN ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 ASN ** S 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 321 ASN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 393 GLN ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 331 ASN ** W 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 GLN X 321 ASN ** X 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 393 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 140 ASN ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 78046 Z= 0.225 Angle : 0.609 14.446 106332 Z= 0.324 Chirality : 0.043 0.294 12479 Planarity : 0.004 0.104 14273 Dihedral : 5.371 52.290 10879 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.65 % Favored : 94.33 % Rotamer: Outliers : 4.75 % Allowed : 15.52 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.54 (0.08), residues: 10399 helix: 1.26 (0.13), residues: 1517 sheet: -1.61 (0.09), residues: 2710 loop : -1.34 (0.07), residues: 6172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 333 HIS 0.005 0.001 HIS Y 193 PHE 0.028 0.002 PHE A 82 TYR 0.021 0.002 TYR D 186 ARG 0.010 0.001 ARG S 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 398 poor density : 1271 time to evaluate : 6.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6426 (tp40) REVERT: A 195 MET cc_start: 0.7600 (mmm) cc_final: 0.7375 (mmp) REVERT: B 95 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7438 (mtt90) REVERT: B 184 THR cc_start: 0.8836 (m) cc_final: 0.8338 (p) REVERT: B 283 TYR cc_start: 0.7351 (p90) cc_final: 0.6803 (p90) REVERT: B 389 LYS cc_start: 0.7019 (mmtt) cc_final: 0.6283 (mttm) REVERT: C 113 MET cc_start: 0.7534 (mmt) cc_final: 0.7188 (mmt) REVERT: D 17 ASP cc_start: 0.7010 (t0) cc_final: 0.6664 (t0) REVERT: D 41 MET cc_start: 0.8292 (mpp) cc_final: 0.7857 (mtm) REVERT: D 172 SER cc_start: 0.8951 (m) cc_final: 0.8734 (p) REVERT: D 371 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8437 (mm) REVERT: D 379 ARG cc_start: 0.5340 (mtt180) cc_final: 0.4882 (mtt180) REVERT: E 49 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8739 (pp) REVERT: E 233 GLU cc_start: 0.5432 (tt0) cc_final: 0.4569 (tp30) REVERT: F 275 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8670 (pt) REVERT: G 100 LYS cc_start: 0.7905 (pttt) cc_final: 0.7628 (pttm) REVERT: G 287 ASP cc_start: 0.6007 (p0) cc_final: 0.5422 (p0) REVERT: G 361 GLU cc_start: 0.7378 (tt0) cc_final: 0.7021 (tt0) REVERT: H 110 MET cc_start: 0.6794 (mpp) cc_final: 0.6347 (mpp) REVERT: H 155 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8153 (tp) REVERT: H 156 ASN cc_start: 0.8040 (p0) cc_final: 0.7410 (p0) REVERT: H 177 TYR cc_start: 0.8324 (p90) cc_final: 0.7864 (p90) REVERT: H 264 ASN cc_start: 0.7766 (t0) cc_final: 0.7493 (t0) REVERT: I 270 THR cc_start: 0.5753 (OUTLIER) cc_final: 0.5476 (p) REVERT: I 373 ASN cc_start: 0.8240 (t0) cc_final: 0.7919 (t0) REVERT: J 49 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8248 (mt) REVERT: J 100 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7199 (mtmp) REVERT: J 274 ASN cc_start: 0.7791 (t0) cc_final: 0.7534 (t0) REVERT: K 62 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: K 318 ASN cc_start: 0.7568 (OUTLIER) cc_final: 0.7306 (m-40) REVERT: L 238 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7212 (mm-30) REVERT: L 366 ASP cc_start: 0.6865 (p0) cc_final: 0.6634 (p0) REVERT: M 153 MET cc_start: 0.7279 (ttt) cc_final: 0.7013 (ttt) REVERT: M 266 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6003 (ttt) REVERT: M 343 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7625 (mm) REVERT: N 41 MET cc_start: 0.8762 (mpt) cc_final: 0.8258 (mpt) REVERT: N 210 TYR cc_start: 0.7723 (m-10) cc_final: 0.7202 (m-80) REVERT: O 40 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7596 (p0) REVERT: O 73 ASP cc_start: 0.6921 (p0) cc_final: 0.6620 (p0) REVERT: O 291 TYR cc_start: 0.7451 (p90) cc_final: 0.7205 (p90) REVERT: O 357 ASN cc_start: 0.6645 (OUTLIER) cc_final: 0.6229 (m-40) REVERT: P 373 ASN cc_start: 0.7910 (t0) cc_final: 0.7677 (t0) REVERT: Q 143 MET cc_start: 0.7307 (ttt) cc_final: 0.7099 (ttt) REVERT: Q 283 TYR cc_start: 0.8389 (p90) cc_final: 0.7874 (p90) REVERT: Q 296 ASP cc_start: 0.7407 (p0) cc_final: 0.7074 (p0) REVERT: Q 392 ASP cc_start: 0.8919 (p0) cc_final: 0.8607 (p0) REVERT: R 113 MET cc_start: 0.8430 (mmm) cc_final: 0.7602 (mmm) REVERT: T 46 LYS cc_start: 0.7052 (mtmm) cc_final: 0.6827 (mtpt) REVERT: T 153 MET cc_start: 0.8055 (mtt) cc_final: 0.7667 (ttm) REVERT: T 210 TYR cc_start: 0.8377 (m-10) cc_final: 0.8175 (m-80) REVERT: T 266 MET cc_start: 0.7087 (mtp) cc_final: 0.6497 (ttt) REVERT: T 273 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6724 (p0) REVERT: U 41 MET cc_start: 0.7606 (mpt) cc_final: 0.6962 (mpt) REVERT: U 73 ASP cc_start: 0.6746 (t0) cc_final: 0.6143 (t0) REVERT: U 223 THR cc_start: 0.7294 (m) cc_final: 0.6990 (p) REVERT: U 308 GLU cc_start: 0.7325 (mp0) cc_final: 0.6987 (mp0) REVERT: V 81 PHE cc_start: 0.8418 (m-80) cc_final: 0.7800 (m-10) REVERT: V 110 MET cc_start: 0.8287 (mpp) cc_final: 0.8034 (mmm) REVERT: V 113 MET cc_start: 0.8296 (mpp) cc_final: 0.8027 (mtm) REVERT: W 143 MET cc_start: 0.7567 (ttp) cc_final: 0.7181 (ttm) REVERT: W 352 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.5896 (t80) REVERT: X 10 ASN cc_start: 0.8727 (t0) cc_final: 0.8457 (m-40) REVERT: X 354 LYS cc_start: 0.6123 (mmpt) cc_final: 0.5861 (mttt) REVERT: Y 274 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7271 (p0) REVERT: Y 391 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: Z 38 PHE cc_start: 0.8228 (m-80) cc_final: 0.5847 (p90) REVERT: Z 370 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7208 (mm-30) REVERT: Z 381 TYR cc_start: 0.8405 (t80) cc_final: 0.7740 (t80) REVERT: Z 382 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.6924 (mp10) REVERT: Z 389 LYS cc_start: 0.8242 (tttm) cc_final: 0.7957 (tttt) outliers start: 398 outliers final: 287 residues processed: 1544 average time/residue: 0.6583 time to fit residues: 1798.0137 Evaluate side-chains 1507 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1201 time to evaluate : 6.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain H residue 398 LEU Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ASN Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 389 LYS Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 100 LYS Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 322 ASN Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 279 ASN Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 266 MET Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain M residue 363 SER Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 40 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 289 VAL Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 331 ASN Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 357 ASN Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 332 VAL Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 346 THR Chi-restraints excluded: chain Q residue 356 THR Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 388 ILE Chi-restraints excluded: chain Q residue 395 LEU Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 289 VAL Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 302 ASN Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 360 LEU Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain S residue 387 THR Chi-restraints excluded: chain S residue 388 ILE Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 79 ASN Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 273 ASN Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 302 ASN Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 375 ILE Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 236 ILE Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain X residue 137 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 263 LEU Chi-restraints excluded: chain X residue 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 332 VAL Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 376 VAL Chi-restraints excluded: chain X residue 394 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 110 MET Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 383 SER Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 391 GLN Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 356 THR Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 366 ASP Chi-restraints excluded: chain Z residue 382 GLN Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 338 optimal weight: 8.9990 chunk 905 optimal weight: 30.0000 chunk 198 optimal weight: 0.9990 chunk 590 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 1006 optimal weight: 7.9990 chunk 835 optimal weight: 20.0000 chunk 465 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 528 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN D 96 ASN D 156 ASN ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 ASN F 393 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 GLN K 313 GLN L 96 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 322 ASN L 364 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 244 ASN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN N 302 ASN N 331 ASN N 380 ASN ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 193 HIS ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 ASN S 114 GLN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 251 ASN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 393 GLN ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 380 ASN W 386 GLN W 391 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN ** X 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN Y 393 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 140 ASN ** Z 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 78046 Z= 0.317 Angle : 0.650 14.474 106332 Z= 0.348 Chirality : 0.044 0.251 12479 Planarity : 0.004 0.102 14273 Dihedral : 5.514 47.868 10879 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.27 % Favored : 93.71 % Rotamer: Outliers : 5.27 % Allowed : 15.98 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.56 (0.08), residues: 10399 helix: 1.21 (0.13), residues: 1523 sheet: -1.68 (0.09), residues: 2774 loop : -1.30 (0.08), residues: 6102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 207 HIS 0.004 0.001 HIS P 193 PHE 0.034 0.002 PHE A 82 TYR 0.030 0.002 TYR H 381 ARG 0.012 0.001 ARG S 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1678 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 441 poor density : 1237 time to evaluate : 6.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6377 (tp40) REVERT: A 195 MET cc_start: 0.7524 (mmm) cc_final: 0.7289 (mmm) REVERT: B 95 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7639 (mtt90) REVERT: B 184 THR cc_start: 0.8875 (m) cc_final: 0.8419 (p) REVERT: B 283 TYR cc_start: 0.7546 (p90) cc_final: 0.7026 (p90) REVERT: B 389 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6340 (mttm) REVERT: C 113 MET cc_start: 0.7533 (mmt) cc_final: 0.7138 (mmt) REVERT: C 323 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: D 41 MET cc_start: 0.8362 (mpp) cc_final: 0.7980 (mtm) REVERT: D 106 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.6927 (p0) REVERT: D 172 SER cc_start: 0.8956 (m) cc_final: 0.8737 (p) REVERT: D 371 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8503 (mm) REVERT: D 379 ARG cc_start: 0.5464 (mtt180) cc_final: 0.5003 (mtt180) REVERT: E 49 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8826 (pp) REVERT: E 233 GLU cc_start: 0.5425 (tt0) cc_final: 0.4387 (tp30) REVERT: F 275 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8729 (pt) REVERT: G 143 MET cc_start: 0.7051 (tpp) cc_final: 0.6627 (ttt) REVERT: G 287 ASP cc_start: 0.6084 (p0) cc_final: 0.5503 (p0) REVERT: G 361 GLU cc_start: 0.7462 (tt0) cc_final: 0.7095 (tt0) REVERT: H 110 MET cc_start: 0.6816 (mpp) cc_final: 0.6267 (mpp) REVERT: H 155 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8095 (tp) REVERT: H 156 ASN cc_start: 0.8150 (p0) cc_final: 0.7559 (p0) REVERT: H 177 TYR cc_start: 0.8361 (p90) cc_final: 0.7783 (p90) REVERT: H 210 TYR cc_start: 0.7483 (m-80) cc_final: 0.6869 (m-80) REVERT: H 264 ASN cc_start: 0.7778 (t0) cc_final: 0.7570 (t0) REVERT: I 270 THR cc_start: 0.5985 (OUTLIER) cc_final: 0.5703 (p) REVERT: I 373 ASN cc_start: 0.8295 (t0) cc_final: 0.7974 (t0) REVERT: J 49 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8304 (mt) REVERT: J 100 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.6981 (mtmp) REVERT: J 110 MET cc_start: 0.7601 (tpp) cc_final: 0.7190 (tpt) REVERT: J 274 ASN cc_start: 0.7832 (t0) cc_final: 0.7620 (t0) REVERT: K 62 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7959 (m-30) REVERT: K 318 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.7304 (m-40) REVERT: L 366 ASP cc_start: 0.6861 (p0) cc_final: 0.6617 (p0) REVERT: M 153 MET cc_start: 0.7251 (ttt) cc_final: 0.6971 (ttt) REVERT: M 266 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.5895 (ttt) REVERT: M 343 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7666 (mm) REVERT: N 41 MET cc_start: 0.8810 (mpt) cc_final: 0.8356 (mpt) REVERT: N 210 TYR cc_start: 0.7827 (m-10) cc_final: 0.7372 (m-80) REVERT: N 245 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7437 (mp) REVERT: O 40 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7542 (p0) REVERT: O 73 ASP cc_start: 0.7002 (p0) cc_final: 0.6678 (p0) REVERT: O 291 TYR cc_start: 0.7505 (p90) cc_final: 0.7249 (p90) REVERT: O 357 ASN cc_start: 0.6737 (OUTLIER) cc_final: 0.6322 (m-40) REVERT: P 373 ASN cc_start: 0.8046 (t0) cc_final: 0.7691 (t0) REVERT: Q 296 ASP cc_start: 0.7487 (p0) cc_final: 0.7145 (p0) REVERT: Q 392 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8581 (p0) REVERT: R 113 MET cc_start: 0.8471 (mmm) cc_final: 0.7639 (mmm) REVERT: S 41 MET cc_start: 0.1058 (mpt) cc_final: 0.0606 (mpt) REVERT: S 212 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.6099 (p-80) REVERT: S 233 GLU cc_start: 0.8393 (mp0) cc_final: 0.8005 (mp0) REVERT: T 153 MET cc_start: 0.8097 (mtt) cc_final: 0.7408 (ttm) REVERT: T 210 TYR cc_start: 0.8356 (m-10) cc_final: 0.8082 (m-80) REVERT: T 266 MET cc_start: 0.7097 (mtp) cc_final: 0.6379 (ttt) REVERT: T 273 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.7083 (p0) REVERT: U 41 MET cc_start: 0.7652 (mpt) cc_final: 0.6910 (mpt) REVERT: U 73 ASP cc_start: 0.7093 (t0) cc_final: 0.6334 (t0) REVERT: U 308 GLU cc_start: 0.7384 (mp0) cc_final: 0.7052 (mp0) REVERT: V 17 ASP cc_start: 0.7608 (m-30) cc_final: 0.7333 (m-30) REVERT: V 81 PHE cc_start: 0.8464 (m-80) cc_final: 0.7844 (m-10) REVERT: V 110 MET cc_start: 0.8370 (mpp) cc_final: 0.8103 (mmm) REVERT: V 113 MET cc_start: 0.8294 (mpp) cc_final: 0.8071 (mtm) REVERT: W 143 MET cc_start: 0.7932 (ttp) cc_final: 0.7599 (ttm) REVERT: W 352 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.5859 (t80) REVERT: W 370 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7865 (mm-30) REVERT: X 10 ASN cc_start: 0.8737 (t0) cc_final: 0.8457 (m110) REVERT: Y 391 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7372 (mp10) REVERT: Z 38 PHE cc_start: 0.8254 (m-80) cc_final: 0.5896 (p90) REVERT: Z 381 TYR cc_start: 0.8391 (t80) cc_final: 0.7778 (t80) REVERT: Z 382 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: Z 389 LYS cc_start: 0.8245 (tttm) cc_final: 0.7951 (tttt) outliers start: 441 outliers final: 334 residues processed: 1534 average time/residue: 0.6503 time to fit residues: 1767.8672 Evaluate side-chains 1539 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 1182 time to evaluate : 8.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ASN Chi-restraints excluded: chain I residue 298 THR Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 389 LYS Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 100 LYS Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 322 ASN Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 279 ASN Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 322 ASN Chi-restraints excluded: chain L residue 357 ASN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 236 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 266 MET Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 363 SER Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 332 VAL Chi-restraints excluded: chain N residue 343 LEU Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 383 SER Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 40 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 62 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 289 VAL Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 331 ASN Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain O residue 357 ASN Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 332 VAL Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 346 THR Chi-restraints excluded: chain Q residue 356 THR Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 388 ILE Chi-restraints excluded: chain Q residue 392 ASP Chi-restraints excluded: chain Q residue 395 LEU Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain Q residue 398 LEU Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 289 VAL Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 360 LEU Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 79 ASN Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 273 ASN Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain T residue 393 GLN Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 302 ASN Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain V residue 375 ILE Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 236 ILE Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain W residue 341 VAL Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain W residue 380 ASN Chi-restraints excluded: chain W residue 391 GLN Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 137 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 263 LEU Chi-restraints excluded: chain X residue 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 332 VAL Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 376 VAL Chi-restraints excluded: chain X residue 394 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 61 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 110 MET Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 383 SER Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 391 GLN Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 356 THR Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 366 ASP Chi-restraints excluded: chain Z residue 382 GLN Chi-restraints excluded: chain Z residue 387 THR Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 970 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 573 optimal weight: 20.0000 chunk 734 optimal weight: 20.0000 chunk 569 optimal weight: 5.9990 chunk 847 optimal weight: 5.9990 chunk 561 optimal weight: 4.9990 chunk 1002 optimal weight: 0.9990 chunk 627 optimal weight: 8.9990 chunk 611 optimal weight: 0.5980 chunk 462 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 98 GLN C 393 GLN D 96 ASN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 GLN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN ** J 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 GLN K 302 ASN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 373 ASN ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 234 ASN ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 351 ASN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 373 ASN ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 GLN X 321 ASN ** X 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 78046 Z= 0.232 Angle : 0.620 16.179 106332 Z= 0.329 Chirality : 0.043 0.265 12479 Planarity : 0.003 0.100 14273 Dihedral : 5.321 47.783 10879 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.67 % Favored : 94.31 % Rotamer: Outliers : 4.80 % Allowed : 16.76 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.41 (0.08), residues: 10399 helix: 1.32 (0.13), residues: 1523 sheet: -1.56 (0.09), residues: 2811 loop : -1.21 (0.08), residues: 6065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 333 HIS 0.003 0.001 HIS I 193 PHE 0.024 0.001 PHE N 42 TYR 0.037 0.002 TYR H 381 ARG 0.012 0.001 ARG S 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 1260 time to evaluate : 6.792 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: A 78 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6236 (tp40) REVERT: B 95 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7570 (mtt90) REVERT: B 184 THR cc_start: 0.8916 (m) cc_final: 0.8441 (p) REVERT: B 283 TYR cc_start: 0.7488 (p90) cc_final: 0.6967 (p90) REVERT: B 389 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6300 (mttm) REVERT: C 113 MET cc_start: 0.7500 (mmt) cc_final: 0.7118 (mmt) REVERT: C 323 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: D 41 MET cc_start: 0.8341 (mpp) cc_final: 0.7897 (mtm) REVERT: D 172 SER cc_start: 0.8961 (m) cc_final: 0.8743 (p) REVERT: D 371 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8474 (mm) REVERT: D 379 ARG cc_start: 0.5374 (mtt180) cc_final: 0.4958 (mtt180) REVERT: E 49 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8778 (pp) REVERT: E 233 GLU cc_start: 0.5373 (tt0) cc_final: 0.4495 (tp30) REVERT: G 143 MET cc_start: 0.6791 (tpp) cc_final: 0.6416 (ttt) REVERT: G 287 ASP cc_start: 0.5729 (p0) cc_final: 0.5261 (p0) REVERT: H 110 MET cc_start: 0.6774 (mpp) cc_final: 0.6212 (mpp) REVERT: H 156 ASN cc_start: 0.8149 (p0) cc_final: 0.7529 (p0) REVERT: H 177 TYR cc_start: 0.8365 (p90) cc_final: 0.7776 (p90) REVERT: H 210 TYR cc_start: 0.7531 (m-80) cc_final: 0.7249 (m-80) REVERT: I 270 THR cc_start: 0.5901 (OUTLIER) cc_final: 0.5629 (p) REVERT: I 373 ASN cc_start: 0.8305 (t0) cc_final: 0.7964 (t0) REVERT: J 49 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8243 (mt) REVERT: J 100 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7139 (mtmp) REVERT: K 62 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: K 318 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: L 366 ASP cc_start: 0.6701 (p0) cc_final: 0.6435 (p0) REVERT: M 266 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.5952 (ttt) REVERT: M 343 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7662 (mm) REVERT: N 41 MET cc_start: 0.8752 (mpt) cc_final: 0.8297 (mpt) REVERT: N 210 TYR cc_start: 0.7762 (m-10) cc_final: 0.7272 (m-80) REVERT: O 40 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7529 (p0) REVERT: O 73 ASP cc_start: 0.6896 (p0) cc_final: 0.6585 (p0) REVERT: O 291 TYR cc_start: 0.7494 (p90) cc_final: 0.7232 (p90) REVERT: O 357 ASN cc_start: 0.6706 (OUTLIER) cc_final: 0.6318 (m-40) REVERT: P 373 ASN cc_start: 0.7902 (t0) cc_final: 0.7674 (t0) REVERT: Q 238 GLU cc_start: 0.7531 (pt0) cc_final: 0.7298 (pt0) REVERT: Q 283 TYR cc_start: 0.8457 (p90) cc_final: 0.7807 (p90) REVERT: Q 296 ASP cc_start: 0.7433 (p0) cc_final: 0.7092 (p0) REVERT: Q 392 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8535 (p0) REVERT: R 113 MET cc_start: 0.8541 (mmm) cc_final: 0.7688 (mmm) REVERT: S 41 MET cc_start: 0.0871 (mpt) cc_final: 0.0442 (mpt) REVERT: S 195 MET cc_start: 0.7043 (tpp) cc_final: 0.6826 (tpp) REVERT: S 212 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.5747 (p-80) REVERT: S 233 GLU cc_start: 0.8312 (mp0) cc_final: 0.7953 (mp0) REVERT: T 59 ASP cc_start: 0.7841 (t0) cc_final: 0.7627 (t0) REVERT: T 153 MET cc_start: 0.8113 (mtt) cc_final: 0.7716 (ttm) REVERT: T 210 TYR cc_start: 0.8272 (m-10) cc_final: 0.8012 (m-80) REVERT: T 266 MET cc_start: 0.7123 (mtp) cc_final: 0.6435 (ttt) REVERT: T 273 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6863 (p0) REVERT: U 41 MET cc_start: 0.7616 (mpt) cc_final: 0.6927 (mpt) REVERT: U 73 ASP cc_start: 0.6855 (t0) cc_final: 0.6195 (t0) REVERT: U 308 GLU cc_start: 0.7351 (mp0) cc_final: 0.7047 (mp0) REVERT: V 17 ASP cc_start: 0.7722 (m-30) cc_final: 0.7461 (m-30) REVERT: V 81 PHE cc_start: 0.8424 (m-80) cc_final: 0.7808 (m-10) REVERT: V 110 MET cc_start: 0.8336 (mpp) cc_final: 0.8127 (mmm) REVERT: V 113 MET cc_start: 0.8262 (mpp) cc_final: 0.7857 (mtm) REVERT: W 352 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5783 (t80) REVERT: X 10 ASN cc_start: 0.8684 (t0) cc_final: 0.8396 (m-40) REVERT: Y 143 MET cc_start: 0.7469 (ttt) cc_final: 0.7057 (ttt) REVERT: Y 391 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: Z 38 PHE cc_start: 0.8255 (m-80) cc_final: 0.5961 (p90) REVERT: Z 381 TYR cc_start: 0.8380 (t80) cc_final: 0.7764 (t80) REVERT: Z 382 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: Z 389 LYS cc_start: 0.8254 (tttm) cc_final: 0.7966 (tttm) outliers start: 402 outliers final: 316 residues processed: 1532 average time/residue: 0.6579 time to fit residues: 1781.5130 Evaluate side-chains 1523 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1188 time to evaluate : 6.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ASN Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 389 LYS Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 100 LYS Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 322 ASN Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 279 ASN Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 357 ASN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 236 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 266 MET Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 363 SER Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 343 LEU Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 40 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 289 VAL Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 331 ASN Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain O residue 357 ASN Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 194 ASP Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 332 VAL Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 346 THR Chi-restraints excluded: chain Q residue 356 THR Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 388 ILE Chi-restraints excluded: chain Q residue 392 ASP Chi-restraints excluded: chain Q residue 395 LEU Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain Q residue 398 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 175 ASP Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 289 VAL Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 302 ASN Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 360 LEU Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 79 ASN Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 114 GLN Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 237 LEU Chi-restraints excluded: chain T residue 273 ASN Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain T residue 393 GLN Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 234 ASN Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 302 ASN Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 236 ILE Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain W residue 341 VAL Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain W residue 380 ASN Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 137 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 263 LEU Chi-restraints excluded: chain X residue 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 313 GLN Chi-restraints excluded: chain X residue 332 VAL Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 344 LEU Chi-restraints excluded: chain X residue 376 VAL Chi-restraints excluded: chain X residue 394 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 110 MET Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 383 SER Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 391 GLN Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 356 THR Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 366 ASP Chi-restraints excluded: chain Z residue 382 GLN Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 620 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 chunk 598 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 637 optimal weight: 7.9990 chunk 682 optimal weight: 6.9990 chunk 495 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 787 optimal weight: 0.3980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 274 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 98 GLN C 393 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 ASN ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN ** J 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 393 GLN ** U 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN W 380 ASN W 391 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 GLN X 321 ASN ** X 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 302 ASN Y 357 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 140 ASN ** Z 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 78046 Z= 0.244 Angle : 0.623 16.778 106332 Z= 0.330 Chirality : 0.043 0.302 12479 Planarity : 0.003 0.099 14273 Dihedral : 5.264 46.245 10879 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.92 % Favored : 94.06 % Rotamer: Outliers : 4.85 % Allowed : 17.04 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.35 (0.08), residues: 10399 helix: 1.41 (0.13), residues: 1517 sheet: -1.53 (0.09), residues: 2823 loop : -1.17 (0.08), residues: 6059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 207 HIS 0.003 0.001 HIS I 193 PHE 0.026 0.002 PHE D 38 TYR 0.042 0.002 TYR H 381 ARG 0.009 0.001 ARG S 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1657 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 1251 time to evaluate : 6.729 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: A 78 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6164 (tp40) REVERT: B 95 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7494 (mtt90) REVERT: B 184 THR cc_start: 0.8896 (m) cc_final: 0.8417 (p) REVERT: B 283 TYR cc_start: 0.7590 (p90) cc_final: 0.7073 (p90) REVERT: B 389 LYS cc_start: 0.7042 (mmtt) cc_final: 0.6310 (mttm) REVERT: C 113 MET cc_start: 0.7504 (mmt) cc_final: 0.7117 (mmt) REVERT: C 323 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: D 41 MET cc_start: 0.8361 (mpp) cc_final: 0.7905 (mtm) REVERT: D 172 SER cc_start: 0.8954 (m) cc_final: 0.8748 (p) REVERT: D 371 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8443 (mm) REVERT: D 379 ARG cc_start: 0.5447 (mtt180) cc_final: 0.5059 (mtt180) REVERT: E 49 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8809 (pp) REVERT: E 233 GLU cc_start: 0.5368 (tt0) cc_final: 0.4496 (tp30) REVERT: G 72 LEU cc_start: 0.8835 (mt) cc_final: 0.8632 (mt) REVERT: G 143 MET cc_start: 0.6751 (tpp) cc_final: 0.6430 (ttt) REVERT: H 110 MET cc_start: 0.6748 (mpp) cc_final: 0.6176 (mpp) REVERT: H 156 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7538 (p0) REVERT: H 177 TYR cc_start: 0.8338 (p90) cc_final: 0.7720 (p90) REVERT: H 210 TYR cc_start: 0.7520 (m-80) cc_final: 0.7277 (m-80) REVERT: H 264 ASN cc_start: 0.7663 (t0) cc_final: 0.7400 (t0) REVERT: I 270 THR cc_start: 0.5945 (OUTLIER) cc_final: 0.5673 (p) REVERT: I 373 ASN cc_start: 0.8307 (t0) cc_final: 0.7975 (t0) REVERT: J 49 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8235 (mt) REVERT: J 100 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7202 (mtmp) REVERT: K 62 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: K 118 TYR cc_start: 0.7417 (m-10) cc_final: 0.7064 (m-80) REVERT: K 318 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: L 366 ASP cc_start: 0.6716 (p0) cc_final: 0.6461 (p0) REVERT: M 266 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.5912 (ttt) REVERT: M 343 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7657 (mm) REVERT: N 41 MET cc_start: 0.8750 (mpt) cc_final: 0.8313 (mpt) REVERT: N 210 TYR cc_start: 0.7768 (m-10) cc_final: 0.7308 (m-80) REVERT: O 40 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7474 (p0) REVERT: O 73 ASP cc_start: 0.6916 (p0) cc_final: 0.6602 (p0) REVERT: O 291 TYR cc_start: 0.7473 (p90) cc_final: 0.7199 (p90) REVERT: O 357 ASN cc_start: 0.6739 (OUTLIER) cc_final: 0.6369 (m-40) REVERT: Q 110 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7012 (mmm) REVERT: Q 238 GLU cc_start: 0.7519 (pt0) cc_final: 0.7283 (pt0) REVERT: Q 283 TYR cc_start: 0.8445 (p90) cc_final: 0.7881 (p90) REVERT: Q 296 ASP cc_start: 0.7453 (p0) cc_final: 0.7103 (p0) REVERT: R 113 MET cc_start: 0.8542 (mmm) cc_final: 0.7669 (mmm) REVERT: S 41 MET cc_start: 0.0598 (mpt) cc_final: 0.0198 (mpt) REVERT: S 212 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.5957 (p-80) REVERT: S 233 GLU cc_start: 0.8338 (mp0) cc_final: 0.7987 (mp0) REVERT: T 59 ASP cc_start: 0.7827 (t0) cc_final: 0.7585 (t0) REVERT: T 153 MET cc_start: 0.8040 (mtt) cc_final: 0.7696 (ttm) REVERT: T 210 TYR cc_start: 0.8280 (m-10) cc_final: 0.8008 (m-80) REVERT: T 266 MET cc_start: 0.7147 (mtp) cc_final: 0.6477 (ttt) REVERT: T 273 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.6948 (p0) REVERT: U 41 MET cc_start: 0.7612 (mpt) cc_final: 0.6852 (mpt) REVERT: U 73 ASP cc_start: 0.6980 (t0) cc_final: 0.6554 (t0) REVERT: U 308 GLU cc_start: 0.7275 (mp0) cc_final: 0.6976 (mp0) REVERT: V 78 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6518 (tp40) REVERT: V 81 PHE cc_start: 0.8419 (m-80) cc_final: 0.7819 (m-10) REVERT: V 110 MET cc_start: 0.8405 (mpp) cc_final: 0.8159 (mmm) REVERT: V 113 MET cc_start: 0.8251 (mpp) cc_final: 0.7857 (mtm) REVERT: W 143 MET cc_start: 0.7965 (ttp) cc_final: 0.7645 (ttm) REVERT: W 352 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5835 (t80) REVERT: X 10 ASN cc_start: 0.8677 (t0) cc_final: 0.8387 (m-40) REVERT: Y 143 MET cc_start: 0.7435 (ttt) cc_final: 0.7028 (ttt) REVERT: Z 38 PHE cc_start: 0.8238 (m-80) cc_final: 0.6004 (p90) REVERT: Z 374 MET cc_start: 0.7425 (ttm) cc_final: 0.7188 (ttm) REVERT: Z 381 TYR cc_start: 0.8368 (t80) cc_final: 0.7746 (t80) REVERT: Z 382 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: Z 389 LYS cc_start: 0.8230 (tttm) cc_final: 0.7971 (tttm) outliers start: 406 outliers final: 340 residues processed: 1529 average time/residue: 0.6566 time to fit residues: 1776.8853 Evaluate side-chains 1545 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 1185 time to evaluate : 6.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ASN Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 389 LYS Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 100 LYS Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 322 ASN Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 279 ASN Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 357 ASN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 236 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 266 MET Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 363 SER Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 343 LEU Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 40 ASP Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 289 VAL Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 331 ASN Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain O residue 357 ASN Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 332 VAL Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 2 PHE Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 110 MET Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 346 THR Chi-restraints excluded: chain Q residue 356 THR Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 388 ILE Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain Q residue 398 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 289 VAL Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 302 ASN Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 360 LEU Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 79 ASN Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 114 GLN Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 237 LEU Chi-restraints excluded: chain T residue 273 ASN Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain T residue 393 GLN Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 212 HIS Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 302 ASN Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain U residue 367 LEU Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 236 ILE Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain W residue 341 VAL Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain W residue 380 ASN Chi-restraints excluded: chain W residue 391 GLN Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 137 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 263 LEU Chi-restraints excluded: chain X residue 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 313 GLN Chi-restraints excluded: chain X residue 322 ASN Chi-restraints excluded: chain X residue 332 VAL Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 LEU Chi-restraints excluded: chain X residue 376 VAL Chi-restraints excluded: chain X residue 394 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 110 MET Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 383 SER Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 356 THR Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 366 ASP Chi-restraints excluded: chain Z residue 382 GLN Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 911 optimal weight: 20.0000 chunk 960 optimal weight: 30.0000 chunk 876 optimal weight: 20.0000 chunk 934 optimal weight: 20.0000 chunk 562 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 733 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 844 optimal weight: 7.9990 chunk 883 optimal weight: 9.9990 chunk 930 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 364 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 274 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 98 GLN C 393 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 ASN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN ** I 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN ** L 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 HIS N 331 ASN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 373 ASN T 393 GLN U 234 ASN ** U 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN ** X 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN Y 393 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 78046 Z= 0.298 Angle : 0.652 16.404 106332 Z= 0.346 Chirality : 0.044 0.305 12479 Planarity : 0.004 0.099 14273 Dihedral : 5.347 45.516 10879 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.25 % Favored : 93.73 % Rotamer: Outliers : 4.80 % Allowed : 17.24 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.39 (0.08), residues: 10399 helix: 1.34 (0.13), residues: 1517 sheet: -1.54 (0.09), residues: 2754 loop : -1.21 (0.08), residues: 6128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 207 HIS 0.003 0.001 HIS P 193 PHE 0.030 0.002 PHE A 82 TYR 0.030 0.002 TYR T 381 ARG 0.009 0.001 ARG S 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1600 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 1198 time to evaluate : 6.889 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: A 28 THR cc_start: 0.7414 (OUTLIER) cc_final: 0.6427 (m) REVERT: A 78 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6243 (tp40) REVERT: B 95 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7555 (mtt90) REVERT: B 184 THR cc_start: 0.8929 (m) cc_final: 0.8464 (p) REVERT: B 283 TYR cc_start: 0.7579 (p90) cc_final: 0.7017 (p90) REVERT: B 389 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6335 (mttm) REVERT: C 113 MET cc_start: 0.7513 (mmt) cc_final: 0.7105 (mmt) REVERT: C 323 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6630 (mt-10) REVERT: D 41 MET cc_start: 0.8394 (mpp) cc_final: 0.7976 (mtm) REVERT: D 106 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.6843 (p0) REVERT: D 172 SER cc_start: 0.8957 (m) cc_final: 0.8748 (p) REVERT: D 371 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8490 (mm) REVERT: D 379 ARG cc_start: 0.5482 (mtt180) cc_final: 0.5115 (mtt180) REVERT: E 49 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8819 (pp) REVERT: E 233 GLU cc_start: 0.5394 (tt0) cc_final: 0.4517 (tp30) REVERT: G 143 MET cc_start: 0.6752 (tpp) cc_final: 0.6473 (ttt) REVERT: G 287 ASP cc_start: 0.5783 (p0) cc_final: 0.5297 (p0) REVERT: H 110 MET cc_start: 0.6776 (mpp) cc_final: 0.6216 (mpp) REVERT: H 156 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7603 (p0) REVERT: H 177 TYR cc_start: 0.8350 (p90) cc_final: 0.7689 (p90) REVERT: H 210 TYR cc_start: 0.7446 (m-80) cc_final: 0.7196 (m-80) REVERT: H 264 ASN cc_start: 0.7709 (t0) cc_final: 0.7420 (t0) REVERT: H 370 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7880 (mm-30) REVERT: I 270 THR cc_start: 0.5924 (OUTLIER) cc_final: 0.5642 (p) REVERT: I 373 ASN cc_start: 0.8235 (t0) cc_final: 0.7931 (t0) REVERT: J 100 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7229 (mtmp) REVERT: K 62 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: K 318 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7487 (m110) REVERT: L 366 ASP cc_start: 0.6718 (p0) cc_final: 0.6512 (p0) REVERT: M 266 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6019 (ttt) REVERT: M 343 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7655 (mm) REVERT: N 41 MET cc_start: 0.8742 (mpt) cc_final: 0.8231 (mpt) REVERT: N 210 TYR cc_start: 0.7749 (m-10) cc_final: 0.7290 (m-80) REVERT: O 73 ASP cc_start: 0.6976 (p0) cc_final: 0.6648 (p0) REVERT: O 291 TYR cc_start: 0.7484 (p90) cc_final: 0.7214 (p90) REVERT: O 357 ASN cc_start: 0.6760 (OUTLIER) cc_final: 0.6401 (m-40) REVERT: Q 238 GLU cc_start: 0.7430 (pt0) cc_final: 0.7224 (pt0) REVERT: Q 283 TYR cc_start: 0.8466 (p90) cc_final: 0.7869 (p90) REVERT: Q 296 ASP cc_start: 0.7483 (p0) cc_final: 0.7130 (p0) REVERT: Q 386 GLN cc_start: 0.8256 (mm110) cc_final: 0.8044 (mm110) REVERT: R 113 MET cc_start: 0.8575 (mmm) cc_final: 0.7658 (mmm) REVERT: S 41 MET cc_start: 0.0738 (mpt) cc_final: 0.0273 (mpt) REVERT: S 195 MET cc_start: 0.7051 (tpp) cc_final: 0.6843 (tpp) REVERT: S 212 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.5846 (p-80) REVERT: T 59 ASP cc_start: 0.7821 (t0) cc_final: 0.7586 (t0) REVERT: T 153 MET cc_start: 0.8079 (mtt) cc_final: 0.7783 (ttm) REVERT: T 210 TYR cc_start: 0.8294 (m-10) cc_final: 0.8004 (m-80) REVERT: T 266 MET cc_start: 0.7063 (mtp) cc_final: 0.6422 (ttt) REVERT: T 273 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7289 (p0) REVERT: U 41 MET cc_start: 0.7613 (mpt) cc_final: 0.6863 (mpt) REVERT: U 73 ASP cc_start: 0.6951 (t0) cc_final: 0.6598 (t0) REVERT: U 308 GLU cc_start: 0.7309 (mp0) cc_final: 0.7014 (mp0) REVERT: U 395 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8227 (tt) REVERT: V 78 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6553 (tp40) REVERT: V 81 PHE cc_start: 0.8447 (m-80) cc_final: 0.7834 (m-10) REVERT: V 110 MET cc_start: 0.8418 (mpp) cc_final: 0.8202 (mmm) REVERT: V 113 MET cc_start: 0.8260 (mpp) cc_final: 0.8047 (mtm) REVERT: W 143 MET cc_start: 0.8056 (ttp) cc_final: 0.7738 (ttm) REVERT: W 352 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.5866 (t80) REVERT: W 380 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8518 (p0) REVERT: X 10 ASN cc_start: 0.8702 (t0) cc_final: 0.8408 (m-40) REVERT: Y 143 MET cc_start: 0.7453 (ttt) cc_final: 0.7056 (ttt) REVERT: Z 38 PHE cc_start: 0.8256 (m-80) cc_final: 0.6033 (p90) REVERT: Z 381 TYR cc_start: 0.8373 (t80) cc_final: 0.7811 (t80) REVERT: Z 382 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: Z 389 LYS cc_start: 0.8230 (tttm) cc_final: 0.7958 (tttm) outliers start: 402 outliers final: 352 residues processed: 1480 average time/residue: 0.6624 time to fit residues: 1739.7680 Evaluate side-chains 1547 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 1174 time to evaluate : 6.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 322 ASN Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ASN Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 389 LYS Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain J residue 100 LYS Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 322 ASN Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 378 GLN Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 279 ASN Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 357 ASN Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 236 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 266 MET Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain M residue 354 LYS Chi-restraints excluded: chain M residue 356 THR Chi-restraints excluded: chain M residue 363 SER Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 229 LEU Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 331 ASN Chi-restraints excluded: chain N residue 343 LEU Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 383 SER Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 289 VAL Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 331 ASN Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain O residue 357 ASN Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 332 VAL Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 2 PHE Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 346 THR Chi-restraints excluded: chain Q residue 356 THR Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 388 ILE Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain Q residue 398 LEU Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 247 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 175 ASP Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 289 VAL Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 302 ASN Chi-restraints excluded: chain S residue 315 VAL Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 360 LEU Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 79 ASN Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 114 GLN Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 237 LEU Chi-restraints excluded: chain T residue 273 ASN Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 339 SER Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 212 HIS Chi-restraints excluded: chain U residue 234 ASN Chi-restraints excluded: chain U residue 269 ASN Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 302 ASN Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain U residue 367 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 395 LEU Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 236 ILE Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 278 THR Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain W residue 341 VAL Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain W residue 380 ASN Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 137 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 263 LEU Chi-restraints excluded: chain X residue 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 322 ASN Chi-restraints excluded: chain X residue 332 VAL Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 376 VAL Chi-restraints excluded: chain X residue 394 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 110 MET Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 314 ILE Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 383 SER Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 356 THR Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 366 ASP Chi-restraints excluded: chain Z residue 382 GLN Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 613 optimal weight: 20.0000 chunk 987 optimal weight: 6.9990 chunk 602 optimal weight: 4.9990 chunk 468 optimal weight: 8.9990 chunk 686 optimal weight: 6.9990 chunk 1036 optimal weight: 8.9990 chunk 953 optimal weight: 2.9990 chunk 825 optimal weight: 0.0870 chunk 85 optimal weight: 7.9990 chunk 637 optimal weight: 0.9990 chunk 505 optimal weight: 10.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 98 GLN C 393 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN ** J 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 HIS ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 292 GLN ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 373 ASN T 393 GLN U 234 ASN U 328 GLN ** U 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 373 ASN ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 309 GLN ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN ** W 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 391 GLN ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 GLN X 321 ASN ** X 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 140 ASN ** Z 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 267 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 78046 Z= 0.217 Angle : 0.627 17.325 106332 Z= 0.330 Chirality : 0.043 0.281 12479 Planarity : 0.003 0.098 14273 Dihedral : 5.175 46.112 10879 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.56 % Favored : 94.43 % Rotamer: Outliers : 4.56 % Allowed : 17.75 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.27 (0.08), residues: 10399 helix: 1.51 (0.13), residues: 1517 sheet: -1.49 (0.09), residues: 2806 loop : -1.12 (0.08), residues: 6076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 333 HIS 0.003 0.001 HIS I 193 PHE 0.023 0.001 PHE A 82 TYR 0.032 0.002 TYR T 381 ARG 0.010 0.001 ARG S 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20798 Ramachandran restraints generated. 10399 Oldfield, 0 Emsley, 10399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1638 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 1256 time to evaluate : 6.892 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: A 28 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.6262 (m) REVERT: A 78 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6192 (tp40) REVERT: B 95 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7479 (mtt90) REVERT: B 184 THR cc_start: 0.8859 (m) cc_final: 0.8371 (p) REVERT: B 283 TYR cc_start: 0.7564 (p90) cc_final: 0.7115 (p90) REVERT: B 389 LYS cc_start: 0.7020 (mmtt) cc_final: 0.6292 (mttm) REVERT: C 113 MET cc_start: 0.7484 (mmt) cc_final: 0.7097 (mmt) REVERT: C 323 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6616 (mt-10) REVERT: D 41 MET cc_start: 0.8392 (mpp) cc_final: 0.7941 (mtm) REVERT: D 106 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6780 (p0) REVERT: D 371 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8468 (mm) REVERT: D 379 ARG cc_start: 0.5605 (mtt180) cc_final: 0.5232 (mtt180) REVERT: E 49 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8798 (pp) REVERT: E 233 GLU cc_start: 0.5338 (tt0) cc_final: 0.4469 (tp30) REVERT: G 110 MET cc_start: 0.7982 (mmt) cc_final: 0.7779 (mmt) REVERT: G 143 MET cc_start: 0.6622 (tpp) cc_final: 0.6377 (ttt) REVERT: H 110 MET cc_start: 0.6672 (mpp) cc_final: 0.6059 (mpp) REVERT: H 177 TYR cc_start: 0.8358 (p90) cc_final: 0.7737 (p90) REVERT: H 210 TYR cc_start: 0.7458 (m-80) cc_final: 0.7231 (m-80) REVERT: H 264 ASN cc_start: 0.7695 (t0) cc_final: 0.7347 (t0) REVERT: I 270 THR cc_start: 0.5820 (OUTLIER) cc_final: 0.5556 (p) REVERT: I 373 ASN cc_start: 0.8197 (t0) cc_final: 0.7899 (t0) REVERT: J 100 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7159 (mtmp) REVERT: K 118 TYR cc_start: 0.7421 (m-10) cc_final: 0.7100 (m-80) REVERT: K 318 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7561 (m-40) REVERT: L 105 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7375 (tpp80) REVERT: L 366 ASP cc_start: 0.6770 (p0) cc_final: 0.6493 (p0) REVERT: M 266 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.5989 (ttt) REVERT: M 343 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7655 (mm) REVERT: N 41 MET cc_start: 0.8775 (mpt) cc_final: 0.8324 (mpt) REVERT: N 357 ASN cc_start: 0.7625 (p0) cc_final: 0.7420 (p0) REVERT: O 73 ASP cc_start: 0.6863 (p0) cc_final: 0.6557 (p0) REVERT: O 291 TYR cc_start: 0.7411 (p90) cc_final: 0.7160 (p90) REVERT: Q 238 GLU cc_start: 0.7533 (pt0) cc_final: 0.7311 (pt0) REVERT: Q 283 TYR cc_start: 0.8420 (p90) cc_final: 0.7917 (p90) REVERT: Q 296 ASP cc_start: 0.7433 (p0) cc_final: 0.7074 (p0) REVERT: R 113 MET cc_start: 0.8563 (mmm) cc_final: 0.7709 (mmm) REVERT: S 41 MET cc_start: 0.0651 (mpt) cc_final: 0.0200 (mpt) REVERT: S 153 MET cc_start: 0.7321 (ttm) cc_final: 0.6571 (ttm) REVERT: S 195 MET cc_start: 0.7031 (tpp) cc_final: 0.6815 (tpp) REVERT: S 212 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.5769 (p-80) REVERT: S 233 GLU cc_start: 0.8366 (mp0) cc_final: 0.7952 (mp0) REVERT: T 59 ASP cc_start: 0.7768 (t0) cc_final: 0.7515 (t0) REVERT: T 153 MET cc_start: 0.8052 (mtt) cc_final: 0.7708 (ttm) REVERT: T 210 TYR cc_start: 0.8278 (m-10) cc_final: 0.7998 (m-80) REVERT: T 266 MET cc_start: 0.7029 (mtp) cc_final: 0.6417 (ttt) REVERT: T 273 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.6981 (p0) REVERT: U 41 MET cc_start: 0.7538 (mpt) cc_final: 0.6828 (mpt) REVERT: U 73 ASP cc_start: 0.6813 (t0) cc_final: 0.6582 (t0) REVERT: U 308 GLU cc_start: 0.7375 (mp0) cc_final: 0.7129 (mp0) REVERT: V 78 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6426 (tp40) REVERT: V 81 PHE cc_start: 0.8389 (m-80) cc_final: 0.7911 (m-10) REVERT: V 291 TYR cc_start: 0.7445 (p90) cc_final: 0.7123 (p90) REVERT: V 374 MET cc_start: 0.8315 (tpp) cc_final: 0.8039 (ttt) REVERT: W 352 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5808 (t80) REVERT: X 10 ASN cc_start: 0.8674 (t0) cc_final: 0.8371 (m-40) REVERT: Y 143 MET cc_start: 0.7434 (ttt) cc_final: 0.7029 (ttt) REVERT: Y 167 THR cc_start: 0.7276 (m) cc_final: 0.6714 (p) REVERT: Z 38 PHE cc_start: 0.8245 (m-80) cc_final: 0.6096 (p90) REVERT: Z 266 MET cc_start: 0.7897 (mtm) cc_final: 0.7624 (tmm) REVERT: Z 370 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7362 (mm-30) REVERT: Z 381 TYR cc_start: 0.8357 (t80) cc_final: 0.7791 (t80) REVERT: Z 389 LYS cc_start: 0.8213 (tttm) cc_final: 0.7944 (tttm) outliers start: 382 outliers final: 323 residues processed: 1518 average time/residue: 0.6538 time to fit residues: 1758.7901 Evaluate side-chains 1528 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1189 time to evaluate : 7.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 132 ASN Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 104 ASN Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 283 TYR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 331 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 389 LYS Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 279 ASN Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 389 LYS Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain J residue 100 LYS Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 322 ASN Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 378 GLN Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 187 ASP Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 279 ASN Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 387 THR Chi-restraints excluded: chain L residue 41 MET Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 84 LEU Chi-restraints excluded: chain L residue 105 ARG Chi-restraints excluded: chain L residue 106 ASN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 263 LEU Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 374 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 123 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 236 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 266 MET Chi-restraints excluded: chain M residue 287 ASP Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain M residue 354 LYS Chi-restraints excluded: chain M residue 363 SER Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 88 ASN Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 254 THR Chi-restraints excluded: chain N residue 273 ASN Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 383 SER Chi-restraints excluded: chain N residue 388 ILE Chi-restraints excluded: chain N residue 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 53 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR Chi-restraints excluded: chain O residue 266 MET Chi-restraints excluded: chain O residue 289 VAL Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 331 ASN Chi-restraints excluded: chain O residue 341 VAL Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 332 VAL Chi-restraints excluded: chain P residue 344 LEU Chi-restraints excluded: chain P residue 356 THR Chi-restraints excluded: chain P residue 367 LEU Chi-restraints excluded: chain P residue 397 THR Chi-restraints excluded: chain Q residue 2 PHE Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 227 THR Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 233 GLU Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 308 GLU Chi-restraints excluded: chain Q residue 336 THR Chi-restraints excluded: chain Q residue 346 THR Chi-restraints excluded: chain Q residue 356 THR Chi-restraints excluded: chain Q residue 374 MET Chi-restraints excluded: chain Q residue 388 ILE Chi-restraints excluded: chain Q residue 392 ASP Chi-restraints excluded: chain Q residue 397 THR Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 247 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 336 THR Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 175 ASP Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain S residue 212 HIS Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 287 ASP Chi-restraints excluded: chain S residue 289 VAL Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 302 ASN Chi-restraints excluded: chain S residue 315 VAL Chi-restraints excluded: chain S residue 356 THR Chi-restraints excluded: chain S residue 360 LEU Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 114 GLN Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 237 LEU Chi-restraints excluded: chain T residue 273 ASN Chi-restraints excluded: chain T residue 300 VAL Chi-restraints excluded: chain T residue 339 SER Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain T residue 393 GLN Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 212 HIS Chi-restraints excluded: chain U residue 234 ASN Chi-restraints excluded: chain U residue 269 ASN Chi-restraints excluded: chain U residue 287 ASP Chi-restraints excluded: chain U residue 302 ASN Chi-restraints excluded: chain U residue 357 ASN Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain U residue 367 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 245 ILE Chi-restraints excluded: chain V residue 299 VAL Chi-restraints excluded: chain V residue 346 THR Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 236 ILE Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 278 THR Chi-restraints excluded: chain W residue 302 ASN Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain W residue 341 VAL Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain W residue 391 GLN Chi-restraints excluded: chain X residue 66 THR Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 137 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 194 ASP Chi-restraints excluded: chain X residue 227 THR Chi-restraints excluded: chain X residue 263 LEU Chi-restraints excluded: chain X residue 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 313 GLN Chi-restraints excluded: chain X residue 322 ASN Chi-restraints excluded: chain X residue 332 VAL Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 344 LEU Chi-restraints excluded: chain X residue 376 VAL Chi-restraints excluded: chain X residue 394 ILE Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 47 VAL Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 110 MET Chi-restraints excluded: chain Y residue 196 ASN Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 383 SER Chi-restraints excluded: chain Y residue 388 ILE Chi-restraints excluded: chain Y residue 399 VAL Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 191 ASN Chi-restraints excluded: chain Z residue 194 ASP Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 356 THR Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 366 ASP Chi-restraints excluded: chain Z residue 382 GLN Chi-restraints excluded: chain Z residue 394 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 655 optimal weight: 8.9990 chunk 878 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 760 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 826 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 848 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 152 optimal weight: 0.0980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 98 GLN C 393 GLN ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN ** I 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN ** J 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 GLN ** K 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 386 GLN L 393 GLN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 322 ASN ** M 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 HIS ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN ** N 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 373 ASN T 393 GLN ** U 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 ASN ** W 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN ** X 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 140 ASN ** Z 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.119754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.109261 restraints weight = 191445.905| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.94 r_work: 0.3549 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 78046 Z= 0.305 Angle : 0.755 59.190 106332 Z= 0.428 Chirality : 0.045 1.094 12479 Planarity : 0.005 0.179 14273 Dihedral : 5.182 46.083 10879 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.66 % Favored : 94.33 % Rotamer: Outliers : 4.41 % Allowed : 18.21 % Favored : 77.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.32 % 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: -1.27 (0.08), residues: 10399 helix: 1.51 (0.13), residues: 1517 sheet: -1.49 (0.09), residues: 2806 loop : -1.12 (0.08), residues: 6076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 333 HIS 0.006 0.001 HIS N 193 PHE 0.036 0.001 PHE U 99 TYR 0.026 0.002 TYR T 381 ARG 0.012 0.001 ARG X 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25486.81 seconds wall clock time: 445 minutes 26.11 seconds (26726.11 seconds total)