Starting phenix.real_space_refine on Mon Sep 30 00:54:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/09_2024/6k9q_9952.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/09_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_9952/09_2024/6k9q_9952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/09_2024/6k9q_9952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/09_2024/6k9q_9952.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9q_9952/09_2024/6k9q_9952.cif" } 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. Time to flip 12 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 35.28, per 1000 atoms: 0.46 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.39 Conformation dependent library (CDL) restraints added in 8.1 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: 13.52 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: 61.38 Time building geometry restraints manager: 17.47 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: 0.00 - 3.11: 104138 3.11 - 6.22: 1894 6.22 - 9.33: 245 9.33 - 12.45: 45 12.45 - 15.56: 10 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 3.040 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 Time spend for trying shortcut: 0.00 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 2.240 Check model and map are aligned: 0.470 Set scattering table: 0.570 Process input model: 175.890 Find NCS groups from input model: 3.530 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.170 ------------------------------------------------------------------------------- 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 : 6.248 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: 0.6868 time to fit residues: 2343.1674 Evaluate side-chains 1284 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1269 time to evaluate : 6.257 ------------------------------------------------------------------------------- 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: 5.9990 chunk 788 optimal weight: 6.9990 chunk 437 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 531 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 chunk 815 optimal weight: 8.9990 chunk 315 optimal weight: 9.9990 chunk 495 optimal weight: 20.0000 chunk 606 optimal weight: 9.9990 chunk 944 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 B 79 ASN B 302 ASN B 393 GLN B 400 ASN C 132 ASN C 295 ASN C 393 GLN D 98 GLN D 313 GLN ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN ** E 251 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 351 ASN 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 ASN H 193 HIS ** H 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 391 GLN H 393 GLN 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN K 302 ASN K 318 ASN K 351 ASN K 391 GLN ** L 111 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 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 196 ASN N 267 GLN ** N 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 322 ASN N 331 ASN N 373 ASN O 267 GLN ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 281 ASN O 400 ASN P 328 GLN ** 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 GLN R 331 ASN R 373 ASN R 386 GLN S 67 ASN S 79 ASN ** S 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 251 ASN S 295 ASN S 337 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 302 ASN ** T 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 391 GLN U 292 GLN U 302 ASN ** U 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 156 ASN V 307 GLN ** V 373 ASN ** 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 268 GLN W 281 ASN 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN X 351 ASN Y 264 ASN Y 268 GLN ** Y 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Z 25 ASN Z 140 ASN Z 307 GLN ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 391 GLN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 78046 Z= 0.321 Angle : 0.716 12.603 106332 Z= 0.390 Chirality : 0.046 0.300 12479 Planarity : 0.005 0.110 14273 Dihedral : 6.472 55.620 10889 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.71 % Favored : 94.27 % Rotamer: Outliers : 3.05 % Allowed : 11.06 % Favored : 85.89 % 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: -2.45 (0.07), residues: 10399 helix: -0.35 (0.12), residues: 1504 sheet: -1.98 (0.09), residues: 2790 loop : -1.80 (0.07), residues: 6105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 333 HIS 0.012 0.001 HIS H 193 PHE 0.018 0.002 PHE U 352 TYR 0.028 0.002 TYR J 381 ARG 0.009 0.001 ARG O 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 1637 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1382 time to evaluate : 6.293 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: 0.7803 (mm-40) cc_final: 0.6558 (tp40) REVERT: B 110 MET cc_start: 0.7802 (mmt) cc_final: 0.7511 (ttt) REVERT: B 283 TYR cc_start: 0.7081 (p90) cc_final: 0.6195 (p90) REVERT: B 389 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6350 (mttm) REVERT: C 105 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.6261 (mmt180) REVERT: C 194 ASP cc_start: 0.8397 (p0) cc_final: 0.8151 (p0) REVERT: C 308 GLU cc_start: 0.8198 (pm20) cc_final: 0.7799 (pp20) REVERT: D 4 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7002 (mm-40) REVERT: D 172 SER cc_start: 0.8941 (m) cc_final: 0.8700 (p) REVERT: E 233 GLU cc_start: 0.5473 (tt0) cc_final: 0.4575 (tp30) REVERT: F 49 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8172 (mt) REVERT: F 103 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6880 (mm-30) REVERT: G 287 ASP cc_start: 0.5917 (p0) cc_final: 0.5576 (p0) REVERT: H 155 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8168 (tp) REVERT: H 156 ASN cc_start: 0.7936 (p0) cc_final: 0.7208 (p0) REVERT: H 177 TYR cc_start: 0.8375 (p90) cc_final: 0.8058 (p90) REVERT: I 199 PHE cc_start: 0.7449 (m-80) cc_final: 0.7247 (m-10) REVERT: I 270 THR cc_start: 0.5863 (OUTLIER) cc_final: 0.5589 (p) REVERT: J 274 ASN cc_start: 0.7568 (t0) cc_final: 0.7329 (t0) REVERT: K 78 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6721 (tp-100) REVERT: L 113 MET cc_start: 0.7012 (ttm) cc_final: 0.6737 (ttm) REVERT: L 238 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6915 (mm-30) REVERT: M 113 MET cc_start: 0.7830 (mtp) cc_final: 0.7508 (ptp) REVERT: M 153 MET cc_start: 0.7228 (ttt) cc_final: 0.6956 (ttt) REVERT: M 343 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7712 (mm) REVERT: N 41 MET cc_start: 0.8721 (mpt) cc_final: 0.8030 (mpt) REVERT: N 210 TYR cc_start: 0.7790 (m-10) cc_final: 0.7469 (m-80) REVERT: O 41 MET cc_start: 0.8423 (mpp) cc_final: 0.7787 (mpp) REVERT: O 73 ASP cc_start: 0.6984 (p0) cc_final: 0.6717 (p0) REVERT: O 291 TYR cc_start: 0.7528 (p90) cc_final: 0.7270 (p90) REVERT: O 333 TRP cc_start: 0.8222 (m-10) cc_final: 0.8019 (m-10) REVERT: P 19 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8181 (mm) REVERT: P 373 ASN cc_start: 0.8132 (t0) cc_final: 0.7818 (t0) REVERT: Q 67 ASN cc_start: 0.8424 (m-40) cc_final: 0.7889 (m-40) REVERT: Q 283 TYR cc_start: 0.8377 (p90) cc_final: 0.7951 (p90) REVERT: Q 398 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8756 (pt) REVERT: R 195 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8439 (mmt) REVERT: S 233 GLU cc_start: 0.8406 (mp0) cc_final: 0.8129 (mp0) REVERT: S 273 ASN cc_start: 0.7167 (m-40) cc_final: 0.6888 (p0) REVERT: T 210 TYR cc_start: 0.8459 (m-10) cc_final: 0.8051 (m-80) REVERT: T 266 MET cc_start: 0.7206 (mtp) cc_final: 0.6533 (ttt) REVERT: U 41 MET cc_start: 0.7495 (mpt) cc_final: 0.6841 (mpt) REVERT: U 73 ASP cc_start: 0.7227 (t0) cc_final: 0.6884 (t0) REVERT: U 223 THR cc_start: 0.7274 (m) cc_final: 0.6951 (p) REVERT: V 76 ILE cc_start: 0.6647 (OUTLIER) cc_final: 0.6441 (pp) REVERT: V 81 PHE cc_start: 0.8374 (m-80) cc_final: 0.7626 (m-10) REVERT: V 113 MET cc_start: 0.7994 (mpp) cc_final: 0.7569 (mtm) REVERT: V 136 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8964 (mp) REVERT: W 393 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7584 (tm-30) REVERT: X 79 ASN cc_start: 0.7067 (t0) cc_final: 0.6589 (t0) REVERT: X 354 LYS cc_start: 0.6267 (mmpt) cc_final: 0.5888 (mttt) REVERT: X 386 GLN cc_start: 0.7823 (tp40) cc_final: 0.7322 (tp-100) REVERT: Z 234 ASN cc_start: 0.8098 (p0) cc_final: 0.7516 (p0) REVERT: Z 381 TYR cc_start: 0.8448 (t80) cc_final: 0.7941 (t80) REVERT: Z 386 GLN cc_start: 0.8414 (tp40) cc_final: 0.8029 (tp40) REVERT: Z 389 LYS cc_start: 0.8400 (tttm) cc_final: 0.8109 (tttm) outliers start: 255 outliers final: 150 residues processed: 1544 average time/residue: 0.6765 time to fit residues: 1837.6107 Evaluate side-chains 1339 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1178 time to evaluate : 6.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 183 VAL 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 184 THR 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 4 GLN Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 74 VAL 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 395 LEU Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 136 ILE 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 51 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 374 MET Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain G residue 23 ILE 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 155 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 366 ASP 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 299 VAL Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain J residue 183 VAL 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 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 223 THR Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain L residue 322 ASN Chi-restraints excluded: chain L residue 357 ASN Chi-restraints excluded: chain L residue 374 MET 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 M residue 343 LEU 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 209 VAL 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 76 ILE Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 298 THR Chi-restraints excluded: chain P residue 19 ILE 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 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 375 ILE 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 365 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 386 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 141 THR 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 103 GLU Chi-restraints excluded: chain T residue 209 VAL 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 47 VAL 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 V residue 64 THR Chi-restraints excluded: chain V residue 76 ILE 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 306 GLU Chi-restraints excluded: chain W residue 365 VAL 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 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 325 LEU 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 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 399 VAL Chi-restraints excluded: chain Z residue 74 VAL 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 289 VAL 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: 6.9990 chunk 293 optimal weight: 0.0010 chunk 786 optimal weight: 9.9990 chunk 643 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 946 optimal weight: 3.9990 chunk 1022 optimal weight: 5.9990 chunk 842 optimal weight: 0.9980 chunk 938 optimal weight: 30.0000 chunk 322 optimal weight: 10.0000 chunk 759 optimal weight: 5.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS B 79 ASN B 391 GLN B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 ASN C 393 GLN D 393 GLN ** E 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 ASN F 4 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** 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 ** H 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 GLN H 357 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 313 GLN I 357 ASN I 386 GLN J 79 ASN J 98 GLN J 393 GLN K 313 GLN L 25 ASN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** 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 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 191 ASN N 331 ASN ** N 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 234 ASN ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN P 382 GLN Q 193 HIS ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN ** S 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 337 GLN S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 269 ASN T 321 ASN U 22 ASN U 67 ASN U 386 GLN ** V 373 ASN ** 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 X 25 ASN ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 156 ASN ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 GLN X 321 ASN ** X 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 268 GLN ** Y 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN Y 384 ASN Y 393 GLN Z 140 ASN ** Z 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 307 GLN ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 78046 Z= 0.222 Angle : 0.644 10.255 106332 Z= 0.347 Chirality : 0.044 0.329 12479 Planarity : 0.004 0.107 14273 Dihedral : 5.868 59.995 10880 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.24 % Favored : 94.74 % Rotamer: Outliers : 3.52 % Allowed : 12.91 % Favored : 83.56 % 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: -2.02 (0.08), residues: 10399 helix: 0.44 (0.13), residues: 1512 sheet: -1.85 (0.09), residues: 2852 loop : -1.54 (0.07), residues: 6035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 333 HIS 0.003 0.001 HIS T 212 PHE 0.018 0.002 PHE P 42 TYR 0.025 0.002 TYR A 177 ARG 0.010 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 1666 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1371 time to evaluate : 6.354 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: 0.7470 (mm-40) cc_final: 0.6343 (tp40) REVERT: A 195 MET cc_start: 0.7816 (mmp) cc_final: 0.7325 (mmm) REVERT: A 367 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 283 TYR cc_start: 0.7140 (p90) cc_final: 0.6653 (p90) REVERT: B 389 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6411 (mttm) REVERT: C 105 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.6357 (mmt-90) REVERT: C 113 MET cc_start: 0.7633 (mmt) cc_final: 0.7241 (mmt) REVERT: C 194 ASP cc_start: 0.8382 (p0) cc_final: 0.8143 (p0) REVERT: D 25 ASN cc_start: 0.7708 (m110) cc_final: 0.7442 (m110) REVERT: D 172 SER cc_start: 0.8955 (m) cc_final: 0.8700 (p) REVERT: D 303 TYR cc_start: 0.7873 (m-10) cc_final: 0.7590 (m-10) REVERT: D 379 ARG cc_start: 0.5592 (mtt180) cc_final: 0.5035 (mtt180) REVERT: E 49 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8656 (pp) REVERT: E 233 GLU cc_start: 0.5460 (tt0) cc_final: 0.4535 (tp30) REVERT: F 4 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: F 35 THR cc_start: 0.8252 (m) cc_final: 0.8010 (p) REVERT: G 269 ASN cc_start: 0.5302 (m-40) cc_final: 0.4979 (m110) REVERT: G 287 ASP cc_start: 0.6012 (p0) cc_final: 0.5560 (p0) REVERT: H 110 MET cc_start: 0.7083 (mpp) cc_final: 0.6637 (mpp) REVERT: H 155 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8168 (tp) REVERT: H 156 ASN cc_start: 0.7895 (p0) cc_final: 0.7265 (p0) REVERT: H 177 TYR cc_start: 0.8391 (p90) cc_final: 0.7850 (p90) REVERT: I 199 PHE cc_start: 0.7323 (m-80) cc_final: 0.7039 (m-10) REVERT: I 270 THR cc_start: 0.5779 (OUTLIER) cc_final: 0.5483 (p) REVERT: J 274 ASN cc_start: 0.7476 (t0) cc_final: 0.7259 (t0) REVERT: L 113 MET cc_start: 0.6941 (ttm) cc_final: 0.6691 (ttm) REVERT: L 238 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7141 (mm-30) REVERT: L 400 ASN cc_start: 0.8524 (m-40) cc_final: 0.8132 (m110) REVERT: M 23 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8113 (tp) REVERT: M 49 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8413 (mm) REVERT: M 113 MET cc_start: 0.7751 (mtp) cc_final: 0.7549 (ptp) REVERT: M 153 MET cc_start: 0.7206 (ttt) cc_final: 0.6957 (ttt) REVERT: N 187 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7449 (p0) REVERT: N 210 TYR cc_start: 0.7714 (m-10) cc_final: 0.7398 (m-80) REVERT: O 41 MET cc_start: 0.8455 (mpp) cc_final: 0.7785 (mpp) REVERT: O 73 ASP cc_start: 0.6933 (p0) cc_final: 0.6655 (p0) REVERT: O 78 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7384 (mm-40) REVERT: O 291 TYR cc_start: 0.7505 (p90) cc_final: 0.7284 (p90) REVERT: P 194 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7495 (m-30) REVERT: P 373 ASN cc_start: 0.8042 (t0) cc_final: 0.7710 (t0) REVERT: Q 283 TYR cc_start: 0.8449 (p90) cc_final: 0.8026 (p90) REVERT: Q 296 ASP cc_start: 0.7453 (p0) cc_final: 0.7159 (p0) REVERT: Q 392 ASP cc_start: 0.8765 (p0) cc_final: 0.8527 (p0) REVERT: R 78 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: R 96 ASN cc_start: 0.8313 (t0) cc_final: 0.8033 (t0) REVERT: R 113 MET cc_start: 0.8502 (mmm) cc_final: 0.7866 (mmm) REVERT: R 393 GLN cc_start: 0.8251 (mt0) cc_final: 0.8042 (mt0) REVERT: S 273 ASN cc_start: 0.7051 (m-40) cc_final: 0.6731 (p0) REVERT: S 308 GLU cc_start: 0.8164 (pp20) cc_final: 0.7955 (pp20) REVERT: T 153 MET cc_start: 0.7746 (mtt) cc_final: 0.7327 (ttm) REVERT: T 210 TYR cc_start: 0.8456 (m-10) cc_final: 0.8061 (m-80) REVERT: T 266 MET cc_start: 0.7135 (mtp) cc_final: 0.6595 (ttt) REVERT: T 381 TYR cc_start: 0.8729 (t80) cc_final: 0.8477 (t80) REVERT: U 41 MET cc_start: 0.7534 (mpt) cc_final: 0.6794 (mpt) REVERT: U 73 ASP cc_start: 0.7220 (t0) cc_final: 0.6889 (t0) REVERT: U 223 THR cc_start: 0.7365 (m) cc_final: 0.7068 (p) REVERT: U 308 GLU cc_start: 0.7544 (mp0) cc_final: 0.7050 (mp0) REVERT: V 136 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8972 (mp) REVERT: W 381 TYR cc_start: 0.8950 (t80) cc_final: 0.8750 (t80) REVERT: W 393 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7629 (tm-30) REVERT: X 10 ASN cc_start: 0.8754 (t0) cc_final: 0.8506 (m-40) REVERT: X 194 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7523 (p0) REVERT: X 313 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8356 (mp10) REVERT: X 354 LYS cc_start: 0.6247 (mmpt) cc_final: 0.5833 (mttt) REVERT: X 386 GLN cc_start: 0.7706 (tp40) cc_final: 0.7227 (tp-100) REVERT: Y 143 MET cc_start: 0.7655 (ttt) cc_final: 0.7452 (ttt) REVERT: Y 331 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8541 (t0) REVERT: Y 391 GLN cc_start: 0.7890 (mp10) cc_final: 0.7152 (mp10) REVERT: Z 234 ASN cc_start: 0.8052 (p0) cc_final: 0.7482 (p0) REVERT: Z 370 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7118 (mm-30) REVERT: Z 381 TYR cc_start: 0.8403 (t80) cc_final: 0.7874 (t80) REVERT: Z 382 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7015 (mp10) REVERT: Z 386 GLN cc_start: 0.8517 (tp40) cc_final: 0.8117 (tp40) REVERT: Z 389 LYS cc_start: 0.8345 (tttm) cc_final: 0.8015 (tttm) outliers start: 295 outliers final: 175 residues processed: 1566 average time/residue: 0.6640 time to fit residues: 1841.6754 Evaluate side-chains 1394 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1204 time to evaluate : 6.262 ------------------------------------------------------------------------------- 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 101 LEU 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 9 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 202 THR 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 C residue 76 ILE 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 365 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 65 THR Chi-restraints excluded: chain D residue 76 ILE 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 300 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 4 GLN 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 300 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 390 THR 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 37 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 366 ASP 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 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 242 THR Chi-restraints excluded: chain J residue 376 VAL 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 25 ASN 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 337 GLN 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 23 ILE Chi-restraints excluded: chain M residue 49 LEU 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 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 127 ILE Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 209 VAL 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 76 ILE Chi-restraints excluded: chain O residue 227 THR 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 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 98 GLN Chi-restraints excluded: chain Q residue 150 THR Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 300 VAL 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 23 ILE 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 300 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 243 VAL 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 S residue 388 ILE Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 103 GLU Chi-restraints excluded: chain T residue 203 LYS Chi-restraints excluded: chain T residue 209 VAL 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 51 VAL 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 341 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain V residue 2 PHE 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 278 THR Chi-restraints excluded: chain W residue 306 GLU Chi-restraints excluded: chain X residue 64 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 299 VAL Chi-restraints excluded: chain X residue 313 GLN Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 333 TRP Chi-restraints excluded: chain X residue 341 VAL 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 52 LYS Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 331 ASN 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 200 VAL Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 365 VAL Chi-restraints excluded: chain Z residue 382 GLN 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: 10.0000 chunk 711 optimal weight: 10.0000 chunk 491 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 451 optimal weight: 20.0000 chunk 635 optimal weight: 20.0000 chunk 949 optimal weight: 6.9990 chunk 1005 optimal weight: 3.9990 chunk 496 optimal weight: 0.0000 chunk 899 optimal weight: 30.0000 chunk 270 optimal weight: 8.9990 overall best weight: 5.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 79 ASN B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** E 191 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 393 GLN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN H 129 GLN H 269 ASN H 382 GLN ** 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN J 79 ASN J 98 GLN J 373 ASN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 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 ** M 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 268 GLN N 331 ASN N 386 GLN ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN P 279 ASN P 382 GLN ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 382 GLN ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN R 386 GLN ** S 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 351 ASN ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 331 ASN W 386 GLN W 391 GLN ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 GLN X 321 ASN ** X 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 268 GLN Z 140 ASN Z 156 ASN ** Z 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 78046 Z= 0.308 Angle : 0.658 10.964 106332 Z= 0.357 Chirality : 0.045 0.263 12479 Planarity : 0.004 0.105 14273 Dihedral : 5.785 52.947 10880 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.03 % Rotamer: Outliers : 4.56 % Allowed : 13.49 % Favored : 81.95 % 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: -1.86 (0.08), residues: 10399 helix: 0.74 (0.13), residues: 1517 sheet: -1.82 (0.09), residues: 2800 loop : -1.46 (0.07), residues: 6082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 333 HIS 0.004 0.001 HIS R 193 PHE 0.026 0.002 PHE K 60 TYR 0.020 0.002 TYR M 283 ARG 0.009 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 1653 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 1271 time to evaluate : 6.367 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: A 78 GLN cc_start: 0.7536 (mm-40) cc_final: 0.6557 (tp40) REVERT: B 95 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7335 (mtt90) REVERT: B 110 MET cc_start: 0.7654 (mmp) cc_final: 0.7300 (tpt) REVERT: B 184 THR cc_start: 0.8880 (m) cc_final: 0.8386 (p) REVERT: B 280 GLN cc_start: 0.8053 (pm20) cc_final: 0.7647 (pm20) REVERT: B 283 TYR cc_start: 0.7284 (p90) cc_final: 0.6789 (p90) REVERT: B 389 LYS cc_start: 0.7093 (mmtt) cc_final: 0.6504 (mttm) REVERT: C 194 ASP cc_start: 0.8391 (p0) cc_final: 0.8162 (p0) REVERT: C 308 GLU cc_start: 0.8196 (pm20) cc_final: 0.7967 (pp20) REVERT: D 41 MET cc_start: 0.8294 (mpp) cc_final: 0.7879 (mtm) REVERT: D 172 SER cc_start: 0.8940 (m) cc_final: 0.8693 (p) REVERT: D 379 ARG cc_start: 0.5489 (mtt180) cc_final: 0.4938 (mtt180) REVERT: E 41 MET cc_start: 0.8340 (mmt) cc_final: 0.8024 (mmt) REVERT: E 49 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8784 (pp) REVERT: E 233 GLU cc_start: 0.5433 (tt0) cc_final: 0.4503 (tp30) REVERT: E 292 GLN cc_start: 0.7610 (mt0) cc_final: 0.7377 (pt0) REVERT: E 361 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: F 275 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8743 (pt) REVERT: G 287 ASP cc_start: 0.5909 (p0) cc_final: 0.5468 (p0) REVERT: H 110 MET cc_start: 0.6962 (mpp) cc_final: 0.6446 (mpp) REVERT: H 155 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8081 (tp) REVERT: H 156 ASN cc_start: 0.8031 (p0) cc_final: 0.7349 (p0) REVERT: H 177 TYR cc_start: 0.8402 (p90) cc_final: 0.7683 (p90) REVERT: I 41 MET cc_start: 0.7812 (mpp) cc_final: 0.7476 (mtp) REVERT: I 199 PHE cc_start: 0.7398 (m-80) cc_final: 0.7174 (m-10) REVERT: I 270 THR cc_start: 0.5810 (OUTLIER) cc_final: 0.5529 (p) REVERT: I 306 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: I 373 ASN cc_start: 0.8170 (t0) cc_final: 0.7874 (t0) REVERT: J 49 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8408 (mt) REVERT: J 274 ASN cc_start: 0.7605 (t0) cc_final: 0.7370 (t0) REVERT: K 78 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6633 (tp-100) REVERT: K 318 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7668 (m-40) REVERT: L 113 MET cc_start: 0.7020 (ttm) cc_final: 0.6746 (ttm) REVERT: M 113 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7619 (ptp) REVERT: M 153 MET cc_start: 0.7309 (ttt) cc_final: 0.7043 (ttt) REVERT: M 343 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7682 (mm) REVERT: N 210 TYR cc_start: 0.7725 (m-10) cc_final: 0.7361 (m-80) REVERT: O 78 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7423 (mm-40) REVERT: O 291 TYR cc_start: 0.7502 (p90) cc_final: 0.7259 (p90) REVERT: P 373 ASN cc_start: 0.8064 (t0) cc_final: 0.7723 (t0) REVERT: Q 283 TYR cc_start: 0.8474 (p90) cc_final: 0.7946 (p90) REVERT: Q 296 ASP cc_start: 0.7442 (p0) cc_final: 0.7168 (p0) REVERT: Q 392 ASP cc_start: 0.8765 (p0) cc_final: 0.8402 (p0) REVERT: Q 398 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8744 (pt) REVERT: R 78 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7085 (mt0) REVERT: S 143 MET cc_start: 0.7648 (tpt) cc_final: 0.7324 (tpt) REVERT: S 273 ASN cc_start: 0.7192 (m-40) cc_final: 0.6860 (p0) REVERT: T 153 MET cc_start: 0.7975 (mtt) cc_final: 0.7600 (ttm) REVERT: T 210 TYR cc_start: 0.8419 (m-10) cc_final: 0.8029 (m-80) REVERT: T 266 MET cc_start: 0.7089 (mtp) cc_final: 0.6491 (ttt) REVERT: U 41 MET cc_start: 0.7627 (mpt) cc_final: 0.6961 (mpt) REVERT: U 73 ASP cc_start: 0.7223 (t0) cc_final: 0.6830 (t0) REVERT: U 308 GLU cc_start: 0.7485 (mp0) cc_final: 0.7073 (mp0) REVERT: V 17 ASP cc_start: 0.7585 (m-30) cc_final: 0.7382 (m-30) REVERT: V 81 PHE cc_start: 0.8391 (m-80) cc_final: 0.7702 (m-10) REVERT: W 352 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5942 (t80) REVERT: W 393 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7658 (tm-30) REVERT: X 10 ASN cc_start: 0.8780 (t0) cc_final: 0.8518 (m-40) REVERT: X 194 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7488 (p0) REVERT: X 354 LYS cc_start: 0.6211 (mmpt) cc_final: 0.5756 (mttt) REVERT: X 386 GLN cc_start: 0.7722 (tp40) cc_final: 0.7222 (tp-100) REVERT: Z 234 ASN cc_start: 0.8065 (p0) cc_final: 0.7485 (p0) REVERT: Z 381 TYR cc_start: 0.8419 (t80) cc_final: 0.7761 (t80) REVERT: Z 382 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: Z 386 GLN cc_start: 0.8622 (tp40) cc_final: 0.8183 (tp40) REVERT: Z 389 LYS cc_start: 0.8318 (tttm) cc_final: 0.7993 (tttt) outliers start: 382 outliers final: 249 residues processed: 1531 average time/residue: 0.6744 time to fit residues: 1829.5663 Evaluate side-chains 1450 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1184 time to evaluate : 6.285 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 202 THR 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 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 276 VAL 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 49 LEU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 123 THR 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 E residue 49 LEU 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 308 GLU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 51 VAL 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 289 VAL Chi-restraints excluded: chain F residue 300 VAL 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 288 LEU Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 397 THR 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 101 LEU Chi-restraints excluded: chain H residue 155 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 THR 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 388 ILE Chi-restraints excluded: chain I residue 392 ASP Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 78 GLN 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 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 223 THR 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 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 L residue 393 GLN Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 113 MET 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 86 ASP Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 209 VAL Chi-restraints excluded: chain N residue 243 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 392 ASP Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 23 ILE 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 346 THR 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 194 ASP Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 243 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 64 THR Chi-restraints excluded: chain Q residue 98 GLN Chi-restraints excluded: chain Q residue 150 THR 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 308 GLU 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 382 GLN 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 Q residue 398 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 220 THR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 307 GLN Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 386 GLN 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 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 325 LEU 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 103 GLU Chi-restraints excluded: chain T residue 149 THR Chi-restraints excluded: chain T residue 209 VAL 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 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 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 288 LEU Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 64 THR 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 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 352 PHE Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain W residue 391 GLN Chi-restraints excluded: chain X residue 64 THR 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 302 ASN Chi-restraints excluded: chain X residue 325 LEU 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 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 290 SER Chi-restraints excluded: chain Y residue 296 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 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 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: 4.9990 chunk 570 optimal weight: 9.9990 chunk 14 optimal weight: 0.1980 chunk 748 optimal weight: 8.9990 chunk 414 optimal weight: 9.9990 chunk 857 optimal weight: 8.9990 chunk 694 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 513 optimal weight: 10.0000 chunk 902 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 400 ASN B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** E 191 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 393 GLN ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 382 GLN ** G 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN ** 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN J 98 GLN J 393 GLN ** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 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 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 HIS ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 391 GLN P 67 ASN Q 67 ASN ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 331 ASN ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 ASN R 386 GLN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 328 GLN ** 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 98 GLN ** 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 400 ASN Y 268 GLN Y 357 ASN Z 140 ASN ** Z 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2677 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= 0.245 Angle : 0.633 14.447 106332 Z= 0.340 Chirality : 0.044 0.250 12479 Planarity : 0.004 0.103 14273 Dihedral : 5.578 51.226 10879 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.51 % Favored : 94.47 % Rotamer: Outliers : 4.35 % Allowed : 14.79 % Favored : 80.86 % 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: -1.69 (0.08), residues: 10399 helix: 0.98 (0.13), residues: 1517 sheet: -1.74 (0.09), residues: 2808 loop : -1.35 (0.08), residues: 6074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 333 HIS 0.002 0.001 HIS M 193 PHE 0.025 0.002 PHE K 60 TYR 0.026 0.002 TYR T 381 ARG 0.009 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 1645 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1281 time to evaluate : 6.351 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: A 78 GLN cc_start: 0.7307 (mm-40) cc_final: 0.6401 (tp40) REVERT: A 177 TYR cc_start: 0.6720 (p90) cc_final: 0.6423 (p90) REVERT: B 95 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7251 (mtt90) REVERT: B 110 MET cc_start: 0.7645 (mmp) cc_final: 0.7238 (tpt) REVERT: B 184 THR cc_start: 0.8879 (m) cc_final: 0.8371 (p) REVERT: B 280 GLN cc_start: 0.8131 (pm20) cc_final: 0.7767 (pm20) REVERT: B 283 TYR cc_start: 0.7325 (p90) cc_final: 0.7106 (p90) REVERT: B 389 LYS cc_start: 0.7071 (mmtt) cc_final: 0.6355 (mttm) REVERT: C 194 ASP cc_start: 0.8313 (p0) cc_final: 0.8087 (p0) REVERT: D 41 MET cc_start: 0.8276 (mpp) cc_final: 0.7848 (mtm) REVERT: D 172 SER cc_start: 0.8920 (m) cc_final: 0.8698 (p) REVERT: D 303 TYR cc_start: 0.7968 (m-10) cc_final: 0.7729 (m-10) REVERT: D 371 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8528 (mm) REVERT: D 379 ARG cc_start: 0.5409 (mtt180) cc_final: 0.4942 (mtt180) REVERT: E 49 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8761 (pp) REVERT: E 233 GLU cc_start: 0.5396 (tt0) cc_final: 0.4476 (tp30) REVERT: F 275 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8730 (pt) REVERT: G 287 ASP cc_start: 0.5842 (p0) cc_final: 0.5350 (p0) REVERT: H 110 MET cc_start: 0.6950 (mpp) cc_final: 0.6329 (mpp) REVERT: H 156 ASN cc_start: 0.8054 (p0) cc_final: 0.7352 (p0) REVERT: H 177 TYR cc_start: 0.8401 (p90) cc_final: 0.7655 (p90) REVERT: H 264 ASN cc_start: 0.7780 (t0) cc_final: 0.7514 (t0) REVERT: I 41 MET cc_start: 0.7714 (mpp) cc_final: 0.7500 (mtp) REVERT: I 199 PHE cc_start: 0.7457 (m-80) cc_final: 0.7226 (m-10) REVERT: I 306 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6413 (tm-30) REVERT: I 373 ASN cc_start: 0.8176 (t0) cc_final: 0.7864 (t0) REVERT: J 49 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8370 (mt) REVERT: J 100 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7393 (mtmp) REVERT: J 274 ASN cc_start: 0.7688 (t0) cc_final: 0.7469 (t0) REVERT: K 78 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.6463 (tp-100) REVERT: K 318 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7603 (m-40) REVERT: M 113 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7573 (ptp) REVERT: M 293 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8585 (mm) REVERT: M 343 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7717 (mm) REVERT: N 210 TYR cc_start: 0.7744 (m-10) cc_final: 0.7316 (m-80) REVERT: O 291 TYR cc_start: 0.7508 (p90) cc_final: 0.7246 (p90) REVERT: P 373 ASN cc_start: 0.7993 (t0) cc_final: 0.7724 (t0) REVERT: Q 143 MET cc_start: 0.7250 (ttt) cc_final: 0.7008 (ttp) REVERT: Q 238 GLU cc_start: 0.7387 (pt0) cc_final: 0.7060 (pt0) REVERT: Q 283 TYR cc_start: 0.8442 (p90) cc_final: 0.7944 (p90) REVERT: Q 296 ASP cc_start: 0.7414 (p0) cc_final: 0.7149 (p0) REVERT: Q 392 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8352 (p0) REVERT: Q 398 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8847 (pt) REVERT: R 78 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: R 113 MET cc_start: 0.8594 (mmm) cc_final: 0.7813 (mmm) REVERT: S 143 MET cc_start: 0.7573 (tpt) cc_final: 0.7201 (tpt) REVERT: S 273 ASN cc_start: 0.7179 (m-40) cc_final: 0.6877 (p0) REVERT: T 153 MET cc_start: 0.8079 (mtt) cc_final: 0.7596 (ttm) REVERT: T 210 TYR cc_start: 0.8330 (m-10) cc_final: 0.7904 (m-80) REVERT: T 266 MET cc_start: 0.7158 (mtp) cc_final: 0.6507 (ttt) REVERT: U 41 MET cc_start: 0.7639 (mpt) cc_final: 0.6961 (mpt) REVERT: U 73 ASP cc_start: 0.7123 (t0) cc_final: 0.6852 (t0) REVERT: U 308 GLU cc_start: 0.7472 (mp0) cc_final: 0.7067 (mp0) REVERT: V 81 PHE cc_start: 0.8318 (m-80) cc_final: 0.7626 (m-10) REVERT: V 113 MET cc_start: 0.8263 (mpp) cc_final: 0.7804 (mtm) REVERT: W 46 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.5052 (ptmt) REVERT: W 143 MET cc_start: 0.7674 (ttp) cc_final: 0.7259 (ttm) REVERT: W 352 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.5903 (t80) REVERT: W 393 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7542 (tm-30) REVERT: X 194 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7245 (p0) REVERT: X 291 TYR cc_start: 0.8145 (p90) cc_final: 0.7880 (p90) REVERT: X 354 LYS cc_start: 0.6276 (mmpt) cc_final: 0.5827 (mttt) REVERT: Y 331 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8596 (t0) REVERT: Z 38 PHE cc_start: 0.8250 (m-80) cc_final: 0.5851 (p90) REVERT: Z 234 ASN cc_start: 0.8092 (p0) cc_final: 0.7519 (p0) REVERT: Z 381 TYR cc_start: 0.8404 (t80) cc_final: 0.7739 (t80) REVERT: Z 382 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: Z 386 GLN cc_start: 0.8643 (tp40) cc_final: 0.8176 (tp40) REVERT: Z 389 LYS cc_start: 0.8327 (tttm) cc_final: 0.7994 (tttt) outliers start: 364 outliers final: 256 residues processed: 1522 average time/residue: 0.6579 time to fit residues: 1777.2885 Evaluate side-chains 1461 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1186 time to evaluate : 6.268 ------------------------------------------------------------------------------- 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 61 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 9 LEU 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 183 VAL Chi-restraints excluded: chain B residue 202 THR 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 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 249 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 364 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 76 ILE 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 300 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 388 ILE 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 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 289 VAL Chi-restraints excluded: chain F residue 300 VAL 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 183 VAL 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 G residue 396 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 101 LEU 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 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 149 THR Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 299 VAL 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 183 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 206 GLU 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 372 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 223 THR Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 243 VAL 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 393 GLN Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 113 MET 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 289 VAL Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain M residue 395 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 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 254 THR 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 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 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 356 THR Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR 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 389 LYS 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 67 ASN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 98 GLN Chi-restraints excluded: chain Q residue 150 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 382 GLN 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 53 VAL Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 386 GLN 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 243 VAL 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 325 LEU 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 103 GLU Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 243 VAL 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 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 94 SER Chi-restraints excluded: chain U residue 143 MET Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 288 LEU Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 383 SER Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 84 LEU 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 W residue 35 THR Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 243 VAL Chi-restraints excluded: chain W residue 339 SER 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 64 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 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 325 LEU 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 X residue 398 LEU 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 236 ILE Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 296 ASP Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 331 ASN 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 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 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: 9.9990 chunk 905 optimal weight: 30.0000 chunk 198 optimal weight: 1.9990 chunk 590 optimal weight: 0.0040 chunk 248 optimal weight: 7.9990 chunk 1006 optimal weight: 10.0000 chunk 835 optimal weight: 20.0000 chunk 465 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 528 optimal weight: 9.9990 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 307 GLN B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** E 191 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 382 GLN ** G 396 ASN ** 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN J 98 GLN K 328 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** 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 98 GLN ** M 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN ** M 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 386 GLN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 212 HIS ** T 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 393 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 98 GLN ** 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 393 GLN Z 140 ASN ** Z 269 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: 0.7791 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 78046 Z= 0.270 Angle : 0.643 14.433 106332 Z= 0.344 Chirality : 0.044 0.256 12479 Planarity : 0.004 0.103 14273 Dihedral : 5.519 47.809 10879 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.10 % Rotamer: Outliers : 4.66 % Allowed : 15.00 % Favored : 80.34 % 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: -1.63 (0.08), residues: 10399 helix: 1.01 (0.13), residues: 1523 sheet: -1.69 (0.09), residues: 2743 loop : -1.33 (0.07), residues: 6133 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 0.021 0.002 PHE K 60 TYR 0.021 0.002 TYR E 118 ARG 0.011 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 1625 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 1235 time to evaluate : 6.310 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: 0.7070 (OUTLIER) cc_final: 0.6118 (tp40) REVERT: B 95 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7341 (mtt90) REVERT: B 110 MET cc_start: 0.7663 (mmp) cc_final: 0.7221 (tpt) REVERT: B 184 THR cc_start: 0.8881 (m) cc_final: 0.8375 (p) REVERT: B 280 GLN cc_start: 0.8150 (pm20) cc_final: 0.7777 (pm20) REVERT: B 283 TYR cc_start: 0.7466 (p90) cc_final: 0.7183 (p90) REVERT: B 389 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6366 (mttm) REVERT: C 330 ASP cc_start: 0.6685 (t70) cc_final: 0.6440 (t70) REVERT: D 41 MET cc_start: 0.8330 (mpp) cc_final: 0.7927 (mtm) REVERT: D 172 SER cc_start: 0.8920 (m) cc_final: 0.8700 (p) REVERT: D 303 TYR cc_start: 0.7987 (m-10) cc_final: 0.7741 (m-10) REVERT: D 325 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7548 (mm) REVERT: D 371 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8537 (mm) REVERT: D 379 ARG cc_start: 0.5522 (mtt180) cc_final: 0.5037 (mtt180) REVERT: E 49 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8788 (pp) REVERT: E 233 GLU cc_start: 0.5436 (tt0) cc_final: 0.4529 (tp30) REVERT: E 361 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: F 275 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8778 (pt) REVERT: G 72 LEU cc_start: 0.8776 (mt) cc_final: 0.8498 (mt) REVERT: G 143 MET cc_start: 0.7099 (tpp) cc_final: 0.6367 (ttt) REVERT: G 287 ASP cc_start: 0.5877 (p0) cc_final: 0.5396 (p0) REVERT: H 110 MET cc_start: 0.6955 (mpp) cc_final: 0.6259 (mpp) REVERT: H 156 ASN cc_start: 0.8104 (p0) cc_final: 0.7477 (p0) REVERT: H 177 TYR cc_start: 0.8379 (p90) cc_final: 0.7585 (p90) REVERT: H 210 TYR cc_start: 0.7551 (m-80) cc_final: 0.7005 (m-80) REVERT: H 264 ASN cc_start: 0.7755 (t0) cc_final: 0.7510 (t0) REVERT: I 306 GLU cc_start: 0.6756 (tm-30) cc_final: 0.6402 (tm-30) REVERT: I 373 ASN cc_start: 0.8204 (t0) cc_final: 0.7875 (t0) REVERT: J 49 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8348 (mt) REVERT: J 100 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7217 (mtmp) REVERT: J 274 ASN cc_start: 0.7724 (t0) cc_final: 0.7512 (t0) REVERT: K 318 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7633 (m-40) REVERT: L 70 ARG cc_start: 0.7302 (ptm160) cc_final: 0.6756 (ttp-170) REVERT: M 153 MET cc_start: 0.7062 (ttt) cc_final: 0.6840 (ttt) REVERT: M 293 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8660 (mm) REVERT: M 343 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7701 (mm) REVERT: N 41 MET cc_start: 0.8772 (mpt) cc_final: 0.8382 (mpt) REVERT: N 210 TYR cc_start: 0.7810 (m-10) cc_final: 0.7413 (m-80) REVERT: N 245 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7391 (mp) REVERT: O 291 TYR cc_start: 0.7523 (p90) cc_final: 0.7260 (p90) REVERT: P 373 ASN cc_start: 0.7944 (t0) cc_final: 0.7739 (t0) REVERT: P 389 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8507 (mtmt) REVERT: Q 238 GLU cc_start: 0.7351 (pt0) cc_final: 0.7005 (pt0) REVERT: Q 296 ASP cc_start: 0.7424 (p0) cc_final: 0.7168 (p0) REVERT: Q 392 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8363 (p0) REVERT: R 78 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6746 (mt0) REVERT: R 113 MET cc_start: 0.8585 (mmm) cc_final: 0.7718 (mmm) REVERT: S 143 MET cc_start: 0.7584 (tpt) cc_final: 0.7202 (tpt) REVERT: S 212 HIS cc_start: 0.6662 (OUTLIER) cc_final: 0.6022 (p-80) REVERT: S 273 ASN cc_start: 0.7208 (m-40) cc_final: 0.6885 (p0) REVERT: T 153 MET cc_start: 0.8211 (mtt) cc_final: 0.7524 (ttm) REVERT: T 210 TYR cc_start: 0.8262 (m-10) cc_final: 0.7836 (m-80) REVERT: T 266 MET cc_start: 0.7182 (mtp) cc_final: 0.6463 (ttt) REVERT: U 41 MET cc_start: 0.7645 (mpt) cc_final: 0.6898 (mpt) REVERT: U 73 ASP cc_start: 0.7119 (t0) cc_final: 0.6818 (t0) REVERT: U 308 GLU cc_start: 0.7389 (mp0) cc_final: 0.7020 (mp0) REVERT: V 81 PHE cc_start: 0.8361 (m-80) cc_final: 0.7669 (m-10) REVERT: V 113 MET cc_start: 0.8265 (mpp) cc_final: 0.7813 (mtm) REVERT: W 46 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.4948 (ptmt) REVERT: W 352 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5789 (t80) REVERT: W 393 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7583 (tm-30) REVERT: X 10 ASN cc_start: 0.8733 (t0) cc_final: 0.8447 (m110) REVERT: X 194 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7216 (p0) REVERT: X 354 LYS cc_start: 0.6335 (mmpt) cc_final: 0.5867 (mttt) REVERT: Y 143 MET cc_start: 0.7682 (ttt) cc_final: 0.7357 (ttt) REVERT: Y 167 THR cc_start: 0.7219 (m) cc_final: 0.6657 (p) REVERT: Y 331 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8571 (t0) REVERT: Z 38 PHE cc_start: 0.8271 (m-80) cc_final: 0.5914 (p90) REVERT: Z 234 ASN cc_start: 0.8145 (p0) cc_final: 0.7603 (p0) REVERT: Z 381 TYR cc_start: 0.8390 (t80) cc_final: 0.7711 (t80) REVERT: Z 382 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: Z 386 GLN cc_start: 0.8643 (tp40) cc_final: 0.8171 (tp40) REVERT: Z 389 LYS cc_start: 0.8241 (tttm) cc_final: 0.7937 (tttt) outliers start: 390 outliers final: 295 residues processed: 1496 average time/residue: 0.6522 time to fit residues: 1728.5133 Evaluate side-chains 1502 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1186 time to evaluate : 6.263 ------------------------------------------------------------------------------- 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 61 THR 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 183 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 76 ILE 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 183 VAL Chi-restraints excluded: chain B residue 202 THR 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 184 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain D residue 3 SER 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 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 325 LEU 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 136 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 390 THR Chi-restraints excluded: chain F residue 2 PHE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 SER 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 289 VAL Chi-restraints excluded: chain F residue 300 VAL 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 35 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 183 VAL 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 G residue 375 ILE Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 101 LEU 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 366 ASP Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 249 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 183 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 206 GLU 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 372 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 229 LEU Chi-restraints excluded: chain L residue 243 VAL 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 L residue 393 GLN Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 68 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 236 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 332 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 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 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 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 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR 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 346 THR 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 237 LEU Chi-restraints excluded: chain P residue 243 VAL 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 389 LYS 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 98 GLN 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 375 ILE Chi-restraints excluded: chain Q residue 382 GLN 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 R residue 23 ILE Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain R residue 84 LEU 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 288 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 386 GLN 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 212 HIS Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 276 VAL 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 325 LEU 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 103 GLU Chi-restraints excluded: chain T residue 114 GLN Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 237 LEU Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 371 LEU 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 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 94 SER Chi-restraints excluded: chain U residue 183 VAL Chi-restraints excluded: chain U residue 288 LEU Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 64 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 W residue 35 THR Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 53 VAL 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 306 GLU Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 341 VAL Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain X residue 64 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 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 325 LEU 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 X residue 398 LEU 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 236 ILE Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 296 ASP Chi-restraints excluded: chain Y residue 331 ASN 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 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 382 GLN 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: 4.9990 chunk 113 optimal weight: 9.9990 chunk 573 optimal weight: 6.9990 chunk 734 optimal weight: 20.0000 chunk 569 optimal weight: 4.9990 chunk 847 optimal weight: 0.9980 chunk 561 optimal weight: 5.9990 chunk 1002 optimal weight: 5.9990 chunk 627 optimal weight: 7.9990 chunk 611 optimal weight: 7.9990 chunk 462 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 400 ASN B 400 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** E 191 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 396 ASN ** 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN L 111 GLN ** L 191 ASN ** 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 400 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN M 154 GLN M 156 ASN M 373 ASN ** M 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 302 ASN N 331 ASN ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN ** Q 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 386 GLN S 15 ASN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 309 GLN T 393 GLN ** V 373 ASN ** 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** X 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN ** X 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN Y 393 GLN Z 111 GLN ** Z 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 78046 Z= 0.258 Angle : 0.643 15.767 106332 Z= 0.342 Chirality : 0.044 0.276 12479 Planarity : 0.004 0.102 14273 Dihedral : 5.444 47.040 10879 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.71 % Favored : 94.27 % Rotamer: Outliers : 4.48 % Allowed : 15.65 % Favored : 79.87 % 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: -1.53 (0.08), residues: 10399 helix: 1.07 (0.13), residues: 1523 sheet: -1.61 (0.09), residues: 2734 loop : -1.26 (0.08), residues: 6142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 207 HIS 0.003 0.001 HIS C 212 PHE 0.032 0.002 PHE A 82 TYR 0.030 0.002 TYR I 186 ARG 0.009 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 1645 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 1270 time to evaluate : 6.306 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: 0.6956 (OUTLIER) cc_final: 0.6137 (tp40) REVERT: B 95 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7508 (mtt90) REVERT: B 110 MET cc_start: 0.7605 (mmp) cc_final: 0.7157 (tpt) REVERT: B 184 THR cc_start: 0.8922 (m) cc_final: 0.8401 (p) REVERT: B 280 GLN cc_start: 0.8152 (pm20) cc_final: 0.7772 (pm20) REVERT: B 283 TYR cc_start: 0.7513 (p90) cc_final: 0.7237 (p90) REVERT: B 389 LYS cc_start: 0.7095 (mmtt) cc_final: 0.6383 (mttm) REVERT: D 41 MET cc_start: 0.8348 (mpp) cc_final: 0.7938 (mtm) REVERT: D 172 SER cc_start: 0.8916 (m) cc_final: 0.8696 (p) REVERT: D 303 TYR cc_start: 0.7974 (m-10) cc_final: 0.7743 (m-10) REVERT: D 325 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7621 (mm) REVERT: D 371 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8517 (mm) REVERT: D 379 ARG cc_start: 0.5473 (mtt180) cc_final: 0.5067 (mtt180) REVERT: E 49 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8774 (pp) REVERT: E 233 GLU cc_start: 0.5445 (tt0) cc_final: 0.4548 (tp30) REVERT: E 361 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: F 103 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6830 (mm-30) REVERT: F 275 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8725 (pt) REVERT: G 72 LEU cc_start: 0.8847 (mt) cc_final: 0.8608 (mt) REVERT: G 287 ASP cc_start: 0.5808 (p0) cc_final: 0.5296 (p0) REVERT: H 110 MET cc_start: 0.6901 (mpp) cc_final: 0.6161 (mpp) REVERT: H 156 ASN cc_start: 0.8131 (p0) cc_final: 0.7514 (p0) REVERT: H 177 TYR cc_start: 0.8355 (p90) cc_final: 0.7488 (p90) REVERT: H 264 ASN cc_start: 0.7765 (t0) cc_final: 0.7515 (t0) REVERT: I 70 ARG cc_start: 0.7353 (ttt90) cc_final: 0.6782 (ttt90) REVERT: I 306 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6384 (tm-30) REVERT: I 311 LEU cc_start: 0.8693 (mp) cc_final: 0.8472 (mp) REVERT: I 373 ASN cc_start: 0.8213 (t0) cc_final: 0.7875 (t0) REVERT: J 49 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8329 (mt) REVERT: J 100 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7168 (mtmp) REVERT: J 274 ASN cc_start: 0.7839 (t0) cc_final: 0.7565 (t0) REVERT: K 308 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: K 318 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7653 (m-40) REVERT: L 105 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7532 (tpp80) REVERT: M 153 MET cc_start: 0.7133 (ttt) cc_final: 0.6904 (ttt) REVERT: M 236 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7348 (mp) REVERT: M 343 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7695 (mm) REVERT: N 41 MET cc_start: 0.8747 (mpt) cc_final: 0.8357 (mpt) REVERT: N 210 TYR cc_start: 0.7728 (m-10) cc_final: 0.7341 (m-80) REVERT: N 245 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7432 (mp) REVERT: O 291 TYR cc_start: 0.7520 (p90) cc_final: 0.7256 (p90) REVERT: P 373 ASN cc_start: 0.7944 (t0) cc_final: 0.7737 (t0) REVERT: P 389 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8385 (mtmt) REVERT: Q 41 MET cc_start: 0.7816 (mpp) cc_final: 0.7326 (mpp) REVERT: Q 238 GLU cc_start: 0.7391 (pt0) cc_final: 0.7078 (pt0) REVERT: Q 296 ASP cc_start: 0.7530 (p0) cc_final: 0.7270 (p0) REVERT: Q 392 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8307 (p0) REVERT: R 78 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6736 (mt0) REVERT: R 113 MET cc_start: 0.8553 (mmm) cc_final: 0.7715 (mmm) REVERT: S 143 MET cc_start: 0.7583 (tpt) cc_final: 0.7309 (tpt) REVERT: S 212 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.5990 (p-80) REVERT: S 273 ASN cc_start: 0.7227 (m-40) cc_final: 0.6904 (p0) REVERT: S 370 GLU cc_start: 0.7513 (mp0) cc_final: 0.6986 (mp0) REVERT: T 153 MET cc_start: 0.8189 (mtt) cc_final: 0.7570 (ttm) REVERT: T 210 TYR cc_start: 0.8246 (m-10) cc_final: 0.7822 (m-80) REVERT: T 266 MET cc_start: 0.7100 (mtp) cc_final: 0.6421 (ttt) REVERT: U 41 MET cc_start: 0.7625 (mpt) cc_final: 0.6936 (mpt) REVERT: U 73 ASP cc_start: 0.7077 (t0) cc_final: 0.6802 (t0) REVERT: U 308 GLU cc_start: 0.7321 (mp0) cc_final: 0.6968 (mp0) REVERT: V 78 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6506 (tp40) REVERT: V 81 PHE cc_start: 0.8338 (m-80) cc_final: 0.7654 (m-10) REVERT: V 113 MET cc_start: 0.8240 (mpp) cc_final: 0.7784 (mtm) REVERT: W 46 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.4947 (ptmt) REVERT: W 352 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5825 (t80) REVERT: W 393 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7599 (tm-30) REVERT: X 10 ASN cc_start: 0.8726 (t0) cc_final: 0.8442 (m110) REVERT: X 194 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7223 (p0) REVERT: X 291 TYR cc_start: 0.8172 (p90) cc_final: 0.7917 (p90) REVERT: X 354 LYS cc_start: 0.6334 (mmpt) cc_final: 0.5872 (mttt) REVERT: Y 143 MET cc_start: 0.7672 (ttt) cc_final: 0.7321 (ttt) REVERT: Y 167 THR cc_start: 0.7240 (m) cc_final: 0.6676 (p) REVERT: Y 331 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8554 (t0) REVERT: Z 38 PHE cc_start: 0.8251 (m-80) cc_final: 0.5958 (p90) REVERT: Z 234 ASN cc_start: 0.8141 (p0) cc_final: 0.7596 (p0) REVERT: Z 361 GLU cc_start: 0.7521 (tp30) cc_final: 0.7303 (tp30) REVERT: Z 381 TYR cc_start: 0.8383 (t80) cc_final: 0.7711 (t80) REVERT: Z 386 GLN cc_start: 0.8658 (tp40) cc_final: 0.8201 (tp40) REVERT: Z 389 LYS cc_start: 0.8276 (tttm) cc_final: 0.8014 (tttt) outliers start: 375 outliers final: 298 residues processed: 1518 average time/residue: 0.7145 time to fit residues: 1930.0627 Evaluate side-chains 1517 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 1195 time to evaluate : 6.367 ------------------------------------------------------------------------------- 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 61 THR 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 183 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 76 ILE 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 183 VAL Chi-restraints excluded: chain B residue 202 THR 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 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 184 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 364 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 76 ILE Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 325 LEU 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 136 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 SER 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 289 VAL Chi-restraints excluded: chain F residue 300 VAL 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 35 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 183 VAL 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 366 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 41 MET 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 101 LEU 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 366 ASP Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain H residue 401 LEU 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 299 VAL 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 183 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 308 GLU 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 229 LEU Chi-restraints excluded: chain L residue 243 VAL 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 388 ILE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 154 GLN 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 289 VAL Chi-restraints excluded: chain M residue 343 LEU Chi-restraints excluded: chain M residue 395 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 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 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 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 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 346 THR Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 243 VAL 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 389 LYS 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 72 LEU Chi-restraints excluded: chain Q residue 98 GLN 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 382 GLN Chi-restraints excluded: chain Q residue 388 ILE Chi-restraints excluded: chain Q residue 392 ASP Chi-restraints excluded: chain Q residue 398 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain R residue 84 LEU 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 288 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 386 GLN 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 212 HIS Chi-restraints excluded: chain S residue 243 VAL Chi-restraints excluded: chain S residue 270 THR Chi-restraints excluded: chain S residue 276 VAL 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 325 LEU 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 103 GLU Chi-restraints excluded: chain T residue 209 VAL Chi-restraints excluded: chain T residue 237 LEU Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 332 VAL 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 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 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 341 VAL Chi-restraints excluded: chain U residue 367 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 383 SER Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 64 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 375 ILE Chi-restraints excluded: chain W residue 35 THR Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 74 VAL 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 306 GLU Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 341 VAL Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain X residue 64 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 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 325 LEU 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 398 LEU 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 236 ILE Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 296 ASP Chi-restraints excluded: chain Y residue 331 ASN 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 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 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: 3.9990 chunk 400 optimal weight: 2.9990 chunk 598 optimal weight: 0.9990 chunk 301 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 194 optimal weight: 30.0000 chunk 637 optimal weight: 7.9990 chunk 682 optimal weight: 6.9990 chunk 495 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 787 optimal weight: 40.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 400 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN C 98 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 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 G 22 ASN G 25 ASN ** G 396 ASN ** 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN J 98 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** 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 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 GLN M 302 ASN ** M 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN N 380 ASN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN P 292 GLN Q 67 ASN Q 382 GLN ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 ASN R 386 GLN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 382 GLN ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 393 GLN U 309 GLN ** V 373 ASN ** 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 98 GLN ** 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN Y 393 GLN Z 140 ASN ** Z 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3036 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= 0.255 Angle : 0.648 16.259 106332 Z= 0.344 Chirality : 0.044 0.289 12479 Planarity : 0.004 0.145 14273 Dihedral : 5.397 46.126 10879 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.77 % Favored : 94.22 % Rotamer: Outliers : 4.61 % Allowed : 15.78 % Favored : 79.61 % 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: -1.47 (0.08), residues: 10399 helix: 1.10 (0.13), residues: 1525 sheet: -1.55 (0.10), residues: 2693 loop : -1.24 (0.08), residues: 6181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 207 HIS 0.003 0.001 HIS C 212 PHE 0.044 0.002 PHE I 99 TYR 0.045 0.002 TYR H 210 ARG 0.010 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 1629 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1243 time to evaluate : 6.355 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: A 78 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6357 (tp40) REVERT: B 95 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7513 (mtt90) REVERT: B 110 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7154 (tpt) REVERT: B 184 THR cc_start: 0.8839 (m) cc_final: 0.8335 (p) REVERT: B 280 GLN cc_start: 0.8139 (pm20) cc_final: 0.7760 (pm20) REVERT: B 283 TYR cc_start: 0.7506 (p90) cc_final: 0.7110 (p90) REVERT: B 354 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8016 (mttm) REVERT: B 389 LYS cc_start: 0.7076 (mmtt) cc_final: 0.6355 (mttm) REVERT: D 41 MET cc_start: 0.8368 (mpp) cc_final: 0.7955 (mtm) REVERT: D 172 SER cc_start: 0.8950 (m) cc_final: 0.8740 (p) REVERT: D 303 TYR cc_start: 0.7995 (m-10) cc_final: 0.7754 (m-10) REVERT: D 325 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7572 (mm) REVERT: D 371 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8519 (mm) REVERT: D 379 ARG cc_start: 0.5501 (mtt180) cc_final: 0.5110 (mtt180) REVERT: E 49 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8793 (pp) REVERT: E 233 GLU cc_start: 0.5434 (tt0) cc_final: 0.4544 (tp30) REVERT: E 361 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: F 275 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8695 (pt) REVERT: G 110 MET cc_start: 0.7472 (mmm) cc_final: 0.7239 (mmm) REVERT: G 143 MET cc_start: 0.7013 (tpp) cc_final: 0.6332 (ttt) REVERT: H 110 MET cc_start: 0.6852 (mpp) cc_final: 0.6112 (mpp) REVERT: H 156 ASN cc_start: 0.8138 (p0) cc_final: 0.7528 (p0) REVERT: H 177 TYR cc_start: 0.8339 (p90) cc_final: 0.7455 (p90) REVERT: H 210 TYR cc_start: 0.7036 (m-80) cc_final: 0.6559 (m-80) REVERT: H 264 ASN cc_start: 0.7760 (t0) cc_final: 0.7499 (t0) REVERT: I 70 ARG cc_start: 0.7270 (ttt90) cc_final: 0.6683 (ttt90) REVERT: I 306 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6467 (tm-30) REVERT: I 373 ASN cc_start: 0.8229 (t0) cc_final: 0.7887 (t0) REVERT: J 49 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8306 (mt) REVERT: J 100 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7166 (mtmp) REVERT: J 274 ASN cc_start: 0.7810 (t0) cc_final: 0.7590 (t0) REVERT: K 308 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: K 318 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7662 (m-40) REVERT: L 70 ARG cc_start: 0.7079 (ptm160) cc_final: 0.6638 (ttp-170) REVERT: L 105 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7477 (tpp80) REVERT: M 153 MET cc_start: 0.7030 (ttt) cc_final: 0.6794 (ttt) REVERT: M 236 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7398 (mp) REVERT: M 343 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7693 (mm) REVERT: N 41 MET cc_start: 0.8750 (mpt) cc_final: 0.8368 (mpt) REVERT: N 210 TYR cc_start: 0.7731 (m-10) cc_final: 0.7381 (m-80) REVERT: O 291 TYR cc_start: 0.7462 (p90) cc_final: 0.7192 (p90) REVERT: P 389 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8426 (mtmt) REVERT: Q 41 MET cc_start: 0.7933 (mpp) cc_final: 0.7415 (mpp) REVERT: Q 238 GLU cc_start: 0.7438 (pt0) cc_final: 0.7144 (pt0) REVERT: Q 392 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8360 (p0) REVERT: R 78 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6660 (mt0) REVERT: R 113 MET cc_start: 0.8551 (mmm) cc_final: 0.7729 (mmm) REVERT: S 143 MET cc_start: 0.7569 (tpt) cc_final: 0.7284 (tpt) REVERT: S 212 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.5924 (p-80) REVERT: S 273 ASN cc_start: 0.7232 (m-40) cc_final: 0.6899 (p0) REVERT: S 370 GLU cc_start: 0.7525 (mp0) cc_final: 0.7063 (mp0) REVERT: T 153 MET cc_start: 0.8177 (mtt) cc_final: 0.7581 (ttm) REVERT: T 210 TYR cc_start: 0.8242 (m-10) cc_final: 0.7807 (m-80) REVERT: T 266 MET cc_start: 0.7088 (mtp) cc_final: 0.6421 (ttt) REVERT: U 41 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6848 (mpt) REVERT: U 73 ASP cc_start: 0.7077 (t0) cc_final: 0.6828 (t0) REVERT: U 308 GLU cc_start: 0.7341 (mp0) cc_final: 0.6962 (mp0) REVERT: V 78 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6570 (tp40) REVERT: V 81 PHE cc_start: 0.8307 (m-80) cc_final: 0.7630 (m-10) REVERT: V 113 MET cc_start: 0.8223 (mpp) cc_final: 0.7784 (mtm) REVERT: V 153 MET cc_start: 0.6539 (ttt) cc_final: 0.6267 (ttt) REVERT: W 46 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.4934 (ptmt) REVERT: W 352 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.5761 (t80) REVERT: W 393 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7678 (tm-30) REVERT: X 10 ASN cc_start: 0.8704 (t0) cc_final: 0.8412 (m110) REVERT: X 194 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7248 (p0) REVERT: X 354 LYS cc_start: 0.6340 (mmpt) cc_final: 0.5909 (mttt) REVERT: Y 143 MET cc_start: 0.7654 (ttt) cc_final: 0.7298 (ttt) REVERT: Y 167 THR cc_start: 0.7254 (m) cc_final: 0.6695 (p) REVERT: Y 331 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8595 (t0) REVERT: Z 38 PHE cc_start: 0.8247 (m-80) cc_final: 0.5999 (p90) REVERT: Z 234 ASN cc_start: 0.8138 (p0) cc_final: 0.7595 (p0) REVERT: Z 374 MET cc_start: 0.7488 (ttm) cc_final: 0.7237 (ttm) REVERT: Z 381 TYR cc_start: 0.8370 (t80) cc_final: 0.7761 (t80) REVERT: Z 386 GLN cc_start: 0.8662 (tp40) cc_final: 0.8203 (tp40) REVERT: Z 389 LYS cc_start: 0.8274 (tttm) cc_final: 0.8013 (tttt) outliers start: 386 outliers final: 313 residues processed: 1490 average time/residue: 0.6592 time to fit residues: 1741.4245 Evaluate side-chains 1533 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1194 time to evaluate : 6.306 ------------------------------------------------------------------------------- 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 61 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 113 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 76 ILE 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 141 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 202 THR 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 354 LYS 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 184 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 364 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 76 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 325 LEU 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 136 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 SER 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 289 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 395 LEU 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 74 VAL Chi-restraints excluded: chain G residue 183 VAL 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 366 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 41 MET 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 101 LEU 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 366 ASP Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain I residue 78 GLN 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 299 VAL 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 183 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 372 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 111 GLN Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 243 VAL 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 64 THR Chi-restraints excluded: chain M residue 66 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 236 ILE Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 343 LEU 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 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 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 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 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR 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 346 THR Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 243 VAL 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 389 LYS 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 67 ASN Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 98 GLN 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 392 ASP Chi-restraints excluded: chain Q residue 398 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain R residue 84 LEU 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 288 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 386 GLN 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 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 276 VAL 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 325 LEU 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 103 GLU Chi-restraints excluded: chain T residue 114 GLN Chi-restraints excluded: chain T residue 237 LEU Chi-restraints excluded: chain T residue 243 VAL Chi-restraints excluded: chain T residue 332 VAL Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain T residue 388 ILE 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 41 MET 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 367 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 383 SER Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 64 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 W residue 35 THR Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 74 VAL 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 306 GLU Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 341 VAL Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain X residue 64 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 299 VAL Chi-restraints excluded: chain X residue 302 ASN Chi-restraints excluded: chain X residue 325 LEU 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 398 LEU 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 236 ILE Chi-restraints excluded: chain Y residue 290 SER Chi-restraints excluded: chain Y residue 296 ASP Chi-restraints excluded: chain Y residue 331 ASN 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 200 VAL Chi-restraints excluded: chain Z residue 229 LEU Chi-restraints excluded: chain Z residue 238 GLU Chi-restraints excluded: chain Z residue 296 ASP Chi-restraints excluded: chain Z residue 298 THR Chi-restraints excluded: chain Z residue 365 VAL 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: 10.0000 chunk 960 optimal weight: 30.0000 chunk 876 optimal weight: 10.0000 chunk 934 optimal weight: 20.0000 chunk 562 optimal weight: 6.9990 chunk 406 optimal weight: 1.9990 chunk 733 optimal weight: 0.0370 chunk 286 optimal weight: 9.9990 chunk 844 optimal weight: 0.0010 chunk 883 optimal weight: 10.0000 chunk 930 optimal weight: 6.9990 overall best weight: 3.2070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 114 GLN A 393 GLN B 400 ASN C 98 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 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 22 ASN ** G 396 ASN ** 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 273 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN L 98 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 ASN ** 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 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 GLN ** 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** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN Q 364 ASN ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 386 GLN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 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 268 GLN ** X 98 GLN ** 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 302 ASN Y 357 ASN Y 393 GLN ** Z 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3123 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= 0.222 Angle : 0.643 17.026 106332 Z= 0.340 Chirality : 0.044 0.311 12479 Planarity : 0.004 0.139 14273 Dihedral : 5.287 46.744 10879 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.35 % Favored : 94.64 % Rotamer: Outliers : 4.20 % Allowed : 16.69 % Favored : 79.11 % 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: -1.38 (0.08), residues: 10399 helix: 1.19 (0.13), residues: 1513 sheet: -1.49 (0.10), residues: 2697 loop : -1.18 (0.08), residues: 6189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 333 HIS 0.002 0.001 HIS M 193 PHE 0.032 0.001 PHE I 99 TYR 0.031 0.002 TYR I 186 ARG 0.011 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 1635 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 1283 time to evaluate : 6.414 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: A 78 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6239 (tp40) REVERT: A 284 LYS cc_start: 0.8070 (mttp) cc_final: 0.7838 (mtmm) REVERT: B 95 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7368 (mtt90) REVERT: B 110 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7119 (tpt) REVERT: B 184 THR cc_start: 0.8776 (m) cc_final: 0.8267 (p) REVERT: B 280 GLN cc_start: 0.8122 (pm20) cc_final: 0.7750 (pm20) REVERT: B 283 TYR cc_start: 0.7495 (p90) cc_final: 0.7212 (p90) REVERT: B 354 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8007 (mttm) REVERT: B 389 LYS cc_start: 0.7002 (mmtt) cc_final: 0.6271 (mttm) REVERT: D 41 MET cc_start: 0.8342 (mpp) cc_final: 0.7883 (mtm) REVERT: D 172 SER cc_start: 0.8942 (m) cc_final: 0.8740 (p) REVERT: D 303 TYR cc_start: 0.7973 (m-10) cc_final: 0.7751 (m-10) REVERT: D 325 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7476 (mm) REVERT: D 371 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8479 (mm) REVERT: D 379 ARG cc_start: 0.5708 (mtt180) cc_final: 0.5334 (mtt180) REVERT: D 381 TYR cc_start: 0.8206 (t80) cc_final: 0.7751 (t80) REVERT: E 49 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8755 (pp) REVERT: E 233 GLU cc_start: 0.5407 (tt0) cc_final: 0.4524 (tp30) REVERT: F 41 MET cc_start: 0.7451 (mtm) cc_final: 0.7205 (mtm) REVERT: F 103 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6876 (mm-30) REVERT: F 275 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8663 (pt) REVERT: G 143 MET cc_start: 0.6846 (tpp) cc_final: 0.6293 (ttt) REVERT: H 110 MET cc_start: 0.6822 (mpp) cc_final: 0.6080 (mpp) REVERT: H 156 ASN cc_start: 0.8126 (p0) cc_final: 0.7505 (p0) REVERT: H 177 TYR cc_start: 0.8324 (p90) cc_final: 0.7470 (p90) REVERT: H 210 TYR cc_start: 0.7018 (m-80) cc_final: 0.6604 (m-80) REVERT: H 264 ASN cc_start: 0.7659 (t0) cc_final: 0.7449 (t0) REVERT: I 70 ARG cc_start: 0.7266 (ttt90) cc_final: 0.6795 (ttt90) REVERT: I 306 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6541 (tm-30) REVERT: I 373 ASN cc_start: 0.8234 (t0) cc_final: 0.7901 (t0) REVERT: J 49 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8237 (mt) REVERT: J 100 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7178 (mtmp) REVERT: K 308 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: L 70 ARG cc_start: 0.7018 (ptm160) cc_final: 0.6631 (ttp-170) REVERT: L 105 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7434 (tpp80) REVERT: M 153 MET cc_start: 0.7140 (ttt) cc_final: 0.6900 (ttt) REVERT: M 236 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7359 (mp) REVERT: M 343 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7684 (mm) REVERT: N 41 MET cc_start: 0.8750 (mpt) cc_final: 0.8412 (mpt) REVERT: N 210 TYR cc_start: 0.7724 (m-10) cc_final: 0.7373 (m-80) REVERT: O 291 TYR cc_start: 0.7421 (p90) cc_final: 0.7149 (p90) REVERT: Q 41 MET cc_start: 0.7889 (mpp) cc_final: 0.7373 (mpp) REVERT: Q 233 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6337 (tm-30) REVERT: Q 238 GLU cc_start: 0.7456 (pt0) cc_final: 0.7249 (pt0) REVERT: Q 254 THR cc_start: 0.5994 (OUTLIER) cc_final: 0.5760 (t) REVERT: Q 283 TYR cc_start: 0.8474 (p90) cc_final: 0.7949 (p90) REVERT: Q 296 ASP cc_start: 0.7649 (p0) cc_final: 0.7270 (p0) REVERT: R 78 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6807 (mt0) REVERT: R 113 MET cc_start: 0.8533 (mmm) cc_final: 0.7709 (mmm) REVERT: S 143 MET cc_start: 0.7583 (tpt) cc_final: 0.7288 (tpt) REVERT: S 212 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.5731 (p-80) REVERT: S 273 ASN cc_start: 0.7206 (m-40) cc_final: 0.6870 (p0) REVERT: T 153 MET cc_start: 0.8170 (mtt) cc_final: 0.7624 (ttm) REVERT: T 210 TYR cc_start: 0.8209 (m-10) cc_final: 0.7794 (m-80) REVERT: T 266 MET cc_start: 0.7094 (mtp) cc_final: 0.6453 (ttt) REVERT: U 41 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6834 (mpt) REVERT: U 73 ASP cc_start: 0.7012 (t0) cc_final: 0.6803 (t0) REVERT: U 308 GLU cc_start: 0.7329 (mp0) cc_final: 0.7019 (mp0) REVERT: V 78 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6556 (tp40) REVERT: V 81 PHE cc_start: 0.8271 (m-80) cc_final: 0.7617 (m-10) REVERT: V 113 MET cc_start: 0.8224 (mpp) cc_final: 0.7801 (mtm) REVERT: V 153 MET cc_start: 0.6614 (ttt) cc_final: 0.6368 (ttt) REVERT: V 302 ASN cc_start: 0.7718 (m110) cc_final: 0.7509 (m-40) REVERT: W 46 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.4963 (ptmt) REVERT: W 352 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5802 (t80) REVERT: W 393 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7610 (tm-30) REVERT: X 10 ASN cc_start: 0.8689 (t0) cc_final: 0.8398 (m-40) REVERT: X 194 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7259 (p0) REVERT: X 354 LYS cc_start: 0.6265 (mmpt) cc_final: 0.5882 (mttt) REVERT: Y 143 MET cc_start: 0.7639 (ttt) cc_final: 0.7281 (ttt) REVERT: Y 167 THR cc_start: 0.7297 (m) cc_final: 0.6725 (p) REVERT: Y 331 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8534 (t0) REVERT: Z 38 PHE cc_start: 0.8233 (m-80) cc_final: 0.6059 (p90) REVERT: Z 234 ASN cc_start: 0.8129 (p0) cc_final: 0.7592 (p0) REVERT: Z 370 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7416 (mm-30) REVERT: Z 381 TYR cc_start: 0.8372 (t80) cc_final: 0.7759 (t80) REVERT: Z 386 GLN cc_start: 0.8606 (tp40) cc_final: 0.8145 (tp40) REVERT: Z 389 LYS cc_start: 0.8266 (tttm) cc_final: 0.8000 (tttt) outliers start: 352 outliers final: 283 residues processed: 1510 average time/residue: 0.6644 time to fit residues: 1778.3433 Evaluate side-chains 1515 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1209 time to evaluate : 6.333 ------------------------------------------------------------------------------- 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 61 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 113 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 76 ILE 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 141 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 202 THR 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 354 LYS 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 184 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 364 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 123 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 325 LEU 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 300 VAL 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 388 ILE Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 SER 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 289 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 390 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 74 VAL Chi-restraints excluded: chain G residue 183 VAL 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 366 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 41 MET 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 101 LEU 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 366 ASP Chi-restraints excluded: chain H residue 392 ASP Chi-restraints excluded: chain H residue 401 LEU 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 299 VAL 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 183 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 372 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 229 LEU Chi-restraints excluded: chain L residue 243 VAL 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 308 GLU 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 388 ILE Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 74 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 289 VAL Chi-restraints excluded: chain M residue 343 LEU 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 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 343 LEU Chi-restraints excluded: chain N residue 361 GLU 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 76 ILE Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 227 THR 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 346 THR Chi-restraints excluded: chain O residue 349 SER Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain O residue 398 LEU 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 197 VAL Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 243 VAL 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 98 GLN Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 254 THR Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 308 GLU 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 R residue 23 ILE Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain R residue 84 LEU 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 300 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 386 GLN 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 84 LEU 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 276 VAL 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 325 LEU 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 388 ILE Chi-restraints excluded: chain T residue 64 THR 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 237 LEU Chi-restraints excluded: chain T residue 332 VAL Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 371 LEU Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain T residue 393 GLN Chi-restraints excluded: chain U residue 41 MET 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 367 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 383 SER Chi-restraints excluded: chain V residue 2 PHE Chi-restraints excluded: chain V residue 64 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 W residue 35 THR Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 74 VAL 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 306 GLU Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain X residue 64 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 299 VAL Chi-restraints excluded: chain X residue 325 LEU 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 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 290 SER Chi-restraints excluded: chain Y residue 296 ASP Chi-restraints excluded: chain Y residue 331 ASN 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 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 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: 6.9990 chunk 987 optimal weight: 2.9990 chunk 602 optimal weight: 7.9990 chunk 468 optimal weight: 0.0980 chunk 686 optimal weight: 9.9990 chunk 1036 optimal weight: 2.9990 chunk 953 optimal weight: 9.9990 chunk 825 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 637 optimal weight: 0.9980 chunk 505 optimal weight: 30.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 393 GLN B 400 ASN C 98 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 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 22 ASN G 25 ASN ** G 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 ASN ** 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 273 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN ** L 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 GLN L 400 ASN ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** M 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 GLN ** N 268 GLN ** 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** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN P 88 ASN Q 393 GLN R 386 GLN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 393 GLN ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN Y 393 GLN ** Z 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 78046 Z= 0.214 Angle : 0.644 17.426 106332 Z= 0.340 Chirality : 0.044 0.313 12479 Planarity : 0.004 0.137 14273 Dihedral : 5.196 46.130 10879 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.34 % Favored : 94.65 % Rotamer: Outliers : 3.76 % Allowed : 17.21 % Favored : 79.02 % 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: -1.30 (0.08), residues: 10399 helix: 1.24 (0.13), residues: 1517 sheet: -1.45 (0.10), residues: 2725 loop : -1.11 (0.08), residues: 6157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 333 HIS 0.002 0.001 HIS M 193 PHE 0.029 0.001 PHE I 99 TYR 0.024 0.002 TYR R 381 ARG 0.011 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 1597 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1282 time to evaluate : 6.361 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: A 78 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6294 (tp40) REVERT: A 284 LYS cc_start: 0.8048 (mttp) cc_final: 0.7822 (mtmm) REVERT: B 95 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7405 (mtt90) REVERT: B 110 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7079 (tpt) REVERT: B 184 THR cc_start: 0.8757 (m) cc_final: 0.8241 (p) REVERT: B 280 GLN cc_start: 0.8153 (pm20) cc_final: 0.7749 (pm20) REVERT: B 283 TYR cc_start: 0.7572 (p90) cc_final: 0.7280 (p90) REVERT: B 354 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7992 (mttm) REVERT: B 389 LYS cc_start: 0.6962 (mmtt) cc_final: 0.6229 (mttm) REVERT: D 41 MET cc_start: 0.8324 (mpp) cc_final: 0.7856 (mtm) REVERT: D 172 SER cc_start: 0.8950 (m) cc_final: 0.8743 (p) REVERT: D 303 TYR cc_start: 0.7957 (m-10) cc_final: 0.7723 (m-10) REVERT: D 325 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7479 (mm) REVERT: D 371 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8448 (mm) REVERT: D 379 ARG cc_start: 0.5609 (mtt180) cc_final: 0.5068 (mmt90) REVERT: D 381 TYR cc_start: 0.8183 (t80) cc_final: 0.7664 (t80) REVERT: E 49 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8738 (pp) REVERT: E 233 GLU cc_start: 0.5400 (tt0) cc_final: 0.4510 (tp30) REVERT: F 103 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6874 (mm-30) REVERT: G 143 MET cc_start: 0.6783 (tpp) cc_final: 0.6258 (ttt) REVERT: G 287 ASP cc_start: 0.5790 (p0) cc_final: 0.5461 (p0) REVERT: H 110 MET cc_start: 0.6804 (mpp) cc_final: 0.6047 (mpp) REVERT: H 156 ASN cc_start: 0.8113 (p0) cc_final: 0.7486 (p0) REVERT: H 177 TYR cc_start: 0.8318 (p90) cc_final: 0.7462 (p90) REVERT: H 210 TYR cc_start: 0.7087 (m-80) cc_final: 0.6696 (m-80) REVERT: H 264 ASN cc_start: 0.7670 (t0) cc_final: 0.7463 (t0) REVERT: I 70 ARG cc_start: 0.7231 (ttt90) cc_final: 0.6766 (ttt90) REVERT: I 306 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6552 (tm-30) REVERT: J 49 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8182 (mt) REVERT: J 100 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7128 (mtmp) REVERT: K 143 MET cc_start: 0.7712 (tpt) cc_final: 0.7446 (tpt) REVERT: L 105 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7451 (tpp80) REVERT: M 153 MET cc_start: 0.7145 (ttt) cc_final: 0.6891 (ttt) REVERT: M 236 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7561 (mp) REVERT: M 343 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7673 (mm) REVERT: M 374 MET cc_start: 0.7818 (tpp) cc_final: 0.7469 (ttt) REVERT: N 41 MET cc_start: 0.8747 (mpt) cc_final: 0.8428 (mpt) REVERT: N 210 TYR cc_start: 0.7708 (m-10) cc_final: 0.7336 (m-80) REVERT: O 291 TYR cc_start: 0.7501 (p90) cc_final: 0.7191 (p90) REVERT: P 88 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7867 (t0) REVERT: Q 41 MET cc_start: 0.7903 (mpp) cc_final: 0.7462 (mpp) REVERT: Q 67 ASN cc_start: 0.8210 (m-40) cc_final: 0.7837 (m-40) REVERT: Q 233 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6334 (tm-30) REVERT: Q 238 GLU cc_start: 0.7470 (pt0) cc_final: 0.7262 (pt0) REVERT: Q 283 TYR cc_start: 0.8447 (p90) cc_final: 0.7932 (p90) REVERT: Q 392 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8395 (p0) REVERT: Q 402 ARG cc_start: 0.7140 (tpt-90) cc_final: 0.5868 (tpp-160) REVERT: R 78 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6740 (mt0) REVERT: R 113 MET cc_start: 0.8529 (mmm) cc_final: 0.7693 (mmm) REVERT: S 143 MET cc_start: 0.7632 (tpt) cc_final: 0.7321 (tpt) REVERT: S 212 HIS cc_start: 0.6617 (OUTLIER) cc_final: 0.5697 (p-80) REVERT: S 273 ASN cc_start: 0.7209 (m-40) cc_final: 0.6853 (p0) REVERT: T 153 MET cc_start: 0.8199 (mtt) cc_final: 0.7665 (ttm) REVERT: T 210 TYR cc_start: 0.8194 (m-10) cc_final: 0.7772 (m-80) REVERT: T 266 MET cc_start: 0.6908 (mtp) cc_final: 0.6415 (ttt) REVERT: U 41 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6794 (mpt) REVERT: U 308 GLU cc_start: 0.7413 (mp0) cc_final: 0.7094 (mp0) REVERT: V 113 MET cc_start: 0.8218 (mpp) cc_final: 0.7789 (mtm) REVERT: V 302 ASN cc_start: 0.7708 (m110) cc_final: 0.7461 (m-40) REVERT: V 355 LEU cc_start: 0.8225 (tp) cc_final: 0.7881 (mp) REVERT: W 46 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.4909 (ptmt) REVERT: W 57 THR cc_start: 0.8520 (m) cc_final: 0.8293 (p) REVERT: W 352 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5732 (t80) REVERT: W 393 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7628 (tm-30) REVERT: X 10 ASN cc_start: 0.8667 (t0) cc_final: 0.8373 (m-40) REVERT: X 194 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7513 (p0) REVERT: X 354 LYS cc_start: 0.6243 (mmpt) cc_final: 0.5853 (mttt) REVERT: Y 143 MET cc_start: 0.7637 (ttt) cc_final: 0.7288 (ttt) REVERT: Y 167 THR cc_start: 0.7281 (m) cc_final: 0.6692 (p) REVERT: Y 331 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8532 (t0) REVERT: Z 38 PHE cc_start: 0.8218 (m-80) cc_final: 0.6095 (p90) REVERT: Z 234 ASN cc_start: 0.8122 (p0) cc_final: 0.7615 (p0) REVERT: Z 370 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7375 (mm-30) REVERT: Z 381 TYR cc_start: 0.8369 (t80) cc_final: 0.7762 (t80) REVERT: Z 386 GLN cc_start: 0.8600 (tp40) cc_final: 0.8134 (tp40) REVERT: Z 389 LYS cc_start: 0.8364 (tttm) cc_final: 0.8062 (tttt) outliers start: 315 outliers final: 273 residues processed: 1485 average time/residue: 0.6656 time to fit residues: 1752.2807 Evaluate side-chains 1506 residues out of total 8371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1212 time to evaluate : 6.597 ------------------------------------------------------------------------------- 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 61 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 113 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 202 THR 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 354 LYS 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 184 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 364 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 123 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 325 LEU 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 300 VAL 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 388 ILE Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 16 LEU 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 390 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 183 VAL 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 366 ASP Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 396 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 41 MET 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 101 LEU 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 366 ASP Chi-restraints excluded: chain H residue 392 ASP 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 299 VAL 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 183 VAL Chi-restraints excluded: chain J residue 184 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 78 GLN Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 372 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 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 374 MET Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 388 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 74 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 289 VAL Chi-restraints excluded: chain M residue 343 LEU 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 107 LEU Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 129 GLN Chi-restraints excluded: chain N residue 209 VAL 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 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 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 346 THR Chi-restraints excluded: chain O residue 356 THR Chi-restraints excluded: chain O residue 398 LEU Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 88 ASN Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 197 VAL 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 98 GLN Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 254 THR Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 308 GLU Chi-restraints excluded: chain Q residue 346 THR Chi-restraints excluded: chain Q residue 355 LEU 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 R residue 23 ILE Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 78 GLN Chi-restraints excluded: chain R residue 84 LEU 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 300 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 386 GLN 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 84 LEU 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 276 VAL Chi-restraints excluded: chain S residue 289 VAL Chi-restraints excluded: chain S residue 299 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 360 LEU Chi-restraints excluded: chain S residue 375 ILE Chi-restraints excluded: chain S residue 376 VAL Chi-restraints excluded: chain S residue 388 ILE Chi-restraints excluded: chain T residue 64 THR 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 237 LEU Chi-restraints excluded: chain T residue 332 VAL Chi-restraints excluded: chain T residue 365 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain T residue 388 ILE Chi-restraints excluded: chain T residue 390 THR Chi-restraints excluded: chain T residue 393 GLN Chi-restraints excluded: chain U residue 41 MET 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 367 LEU Chi-restraints excluded: chain U residue 371 LEU Chi-restraints excluded: chain U residue 383 SER Chi-restraints excluded: chain V residue 64 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 W residue 35 THR Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 74 VAL 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 306 GLU Chi-restraints excluded: chain W residue 352 PHE Chi-restraints excluded: chain X residue 64 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 299 VAL Chi-restraints excluded: chain X residue 325 LEU 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 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 110 MET Chi-restraints excluded: chain Y residue 236 ILE Chi-restraints excluded: chain Y residue 296 ASP Chi-restraints excluded: chain Y residue 331 ASN 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 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 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: 0.0970 chunk 878 optimal weight: 4.9990 chunk 252 optimal weight: 0.0030 chunk 760 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 826 optimal weight: 20.0000 chunk 345 optimal weight: 6.9990 chunk 848 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 152 optimal weight: 0.3980 overall best weight: 2.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 400 ASN C 98 GLN C 393 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** E 191 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 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 ASN ** 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 273 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** 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 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 ASN ** N 378 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** ** O 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 ASN P 88 ASN P 292 GLN ** Q 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 386 GLN ** S 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 307 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 321 ASN ** X 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN ** Z 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.120525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.110108 restraints weight = 189251.041| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.00 r_work: 0.3565 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.371 78046 Z= 0.261 Angle : 0.773 65.891 106332 Z= 0.437 Chirality : 0.044 0.979 12479 Planarity : 0.005 0.219 14273 Dihedral : 5.197 46.106 10879 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.36 % Favored : 94.63 % Rotamer: Outliers : 3.82 % Allowed : 17.56 % Favored : 78.62 % Cbeta Deviations : 0.03 % 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: -1.30 (0.08), residues: 10399 helix: 1.25 (0.13), residues: 1517 sheet: -1.45 (0.10), residues: 2725 loop : -1.11 (0.08), residues: 6157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 333 HIS 0.002 0.001 HIS M 193 PHE 0.041 0.001 PHE C 82 TYR 0.025 0.002 TYR X 283 ARG 0.009 0.001 ARG S 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25298.67 seconds wall clock time: 435 minutes 35.42 seconds (26135.42 seconds total)