Starting phenix.real_space_refine on Wed Aug 27 03:06:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l01_62682/08_2025/9l01_62682.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l01_62682/08_2025/9l01_62682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l01_62682/08_2025/9l01_62682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l01_62682/08_2025/9l01_62682.map" model { file = "/net/cci-nas-00/data/ceres_data/9l01_62682/08_2025/9l01_62682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l01_62682/08_2025/9l01_62682.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.868 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 216 5.16 5 C 30276 2.51 5 N 8220 2.21 5 O 9288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 48000 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "M" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "A" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "N" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "C" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "O" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "P" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "E" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "Q" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "F" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "R" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "G" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "S" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "H" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "T" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "I" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "U" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "J" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "V" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "K" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "W" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "L" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1038 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "X" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2962 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 12, 'TRANS': 361} Time building chain proxies: 8.76, per 1000 atoms: 0.18 Number of scatterers: 48000 At special positions: 0 Unit cell: (170, 170, 179.52, 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 216 16.00 O 9288 8.00 N 8220 7.00 C 30276 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: 3.46 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11400 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 49 sheets defined 52.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 24 through 37 removed outlier: 3.717A pdb=" N LEU B 28 " --> pdb=" O PRO B 24 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 47 through 61 Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.541A pdb=" N TYR B 76 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'M' and resid 33 through 40 Processing helix chain 'M' and resid 40 through 58 removed outlier: 4.926A pdb=" N ILE M 50 " --> pdb=" O ILE M 46 " (cutoff:3.500A) Proline residue: M 51 - end of helix removed outlier: 3.778A pdb=" N ALA M 57 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY M 58 " --> pdb=" O MET M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 78 removed outlier: 3.688A pdb=" N PHE M 70 " --> pdb=" O ASP M 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR M 77 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS M 78 " --> pdb=" O TRP M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 94 Processing helix chain 'M' and resid 127 through 129 No H-bonds generated for 'chain 'M' and resid 127 through 129' Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.524A pdb=" N GLN M 182 " --> pdb=" O GLN M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 215 removed outlier: 3.518A pdb=" N ILE M 196 " --> pdb=" O ASN M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 250 removed outlier: 3.635A pdb=" N TYR M 237 " --> pdb=" O ASP M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 291 removed outlier: 3.566A pdb=" N GLY M 291 " --> pdb=" O VAL M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 299 Processing helix chain 'M' and resid 309 through 336 removed outlier: 4.314A pdb=" N LEU M 313 " --> pdb=" O GLN M 309 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR M 315 " --> pdb=" O THR M 311 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE M 316 " --> pdb=" O ALA M 312 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG M 329 " --> pdb=" O GLU M 325 " (cutoff:3.500A) Proline residue: M 330 - end of helix Processing helix chain 'M' and resid 337 through 339 No H-bonds generated for 'chain 'M' and resid 337 through 339' Processing helix chain 'M' and resid 356 through 376 Processing helix chain 'M' and resid 381 through 393 Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.705A pdb=" N LEU A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 61 Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.559A pdb=" N TYR A 76 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'N' and resid 33 through 40 Processing helix chain 'N' and resid 40 through 58 removed outlier: 4.908A pdb=" N ILE N 50 " --> pdb=" O ILE N 46 " (cutoff:3.500A) Proline residue: N 51 - end of helix removed outlier: 3.694A pdb=" N ALA N 57 " --> pdb=" O GLU N 53 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY N 58 " --> pdb=" O MET N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 78 removed outlier: 3.685A pdb=" N PHE N 70 " --> pdb=" O ASP N 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR N 77 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS N 78 " --> pdb=" O TRP N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 94 Processing helix chain 'N' and resid 127 through 129 No H-bonds generated for 'chain 'N' and resid 127 through 129' Processing helix chain 'N' and resid 176 through 183 removed outlier: 3.528A pdb=" N GLN N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 215 Processing helix chain 'N' and resid 233 through 250 removed outlier: 3.647A pdb=" N TYR N 237 " --> pdb=" O ASP N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 291 removed outlier: 3.606A pdb=" N GLY N 291 " --> pdb=" O VAL N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 299 Processing helix chain 'N' and resid 313 through 336 removed outlier: 4.980A pdb=" N ARG N 329 " --> pdb=" O GLU N 325 " (cutoff:3.500A) Proline residue: N 330 - end of helix Processing helix chain 'N' and resid 337 through 339 No H-bonds generated for 'chain 'N' and resid 337 through 339' Processing helix chain 'N' and resid 356 through 376 Processing helix chain 'N' and resid 381 through 393 Processing helix chain 'C' and resid 3 through 17 Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.726A pdb=" N LEU C 28 " --> pdb=" O PRO C 24 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 47 through 61 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'O' and resid 33 through 40 Processing helix chain 'O' and resid 40 through 58 removed outlier: 4.923A pdb=" N ILE O 50 " --> pdb=" O ILE O 46 " (cutoff:3.500A) Proline residue: O 51 - end of helix removed outlier: 3.735A pdb=" N ALA O 57 " --> pdb=" O GLU O 53 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY O 58 " --> pdb=" O MET O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 78 removed outlier: 3.710A pdb=" N PHE O 70 " --> pdb=" O ASP O 66 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR O 77 " --> pdb=" O LEU O 73 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS O 78 " --> pdb=" O TRP O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 94 Processing helix chain 'O' and resid 127 through 129 No H-bonds generated for 'chain 'O' and resid 127 through 129' Processing helix chain 'O' and resid 176 through 183 removed outlier: 3.548A pdb=" N GLN O 182 " --> pdb=" O GLN O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 215 Processing helix chain 'O' and resid 233 through 250 removed outlier: 3.671A pdb=" N TYR O 237 " --> pdb=" O ASP O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 274 through 291 removed outlier: 3.637A pdb=" N GLY O 291 " --> pdb=" O VAL O 287 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 299 Processing helix chain 'O' and resid 313 through 336 removed outlier: 4.828A pdb=" N ARG O 329 " --> pdb=" O GLU O 325 " (cutoff:3.500A) Proline residue: O 330 - end of helix Processing helix chain 'O' and resid 337 through 339 No H-bonds generated for 'chain 'O' and resid 337 through 339' Processing helix chain 'O' and resid 356 through 376 Processing helix chain 'O' and resid 381 through 393 Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.713A pdb=" N LEU D 28 " --> pdb=" O PRO D 24 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 37 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.554A pdb=" N TYR D 76 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'P' and resid 33 through 40 Processing helix chain 'P' and resid 40 through 58 removed outlier: 4.908A pdb=" N ILE P 50 " --> pdb=" O ILE P 46 " (cutoff:3.500A) Proline residue: P 51 - end of helix removed outlier: 3.696A pdb=" N ALA P 57 " --> pdb=" O GLU P 53 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY P 58 " --> pdb=" O MET P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 78 removed outlier: 3.703A pdb=" N PHE P 70 " --> pdb=" O ASP P 66 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR P 77 " --> pdb=" O LEU P 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS P 78 " --> pdb=" O TRP P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 94 Processing helix chain 'P' and resid 127 through 129 No H-bonds generated for 'chain 'P' and resid 127 through 129' Processing helix chain 'P' and resid 176 through 183 removed outlier: 3.527A pdb=" N GLN P 182 " --> pdb=" O GLN P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 215 Processing helix chain 'P' and resid 233 through 250 removed outlier: 3.648A pdb=" N TYR P 237 " --> pdb=" O ASP P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 291 removed outlier: 3.612A pdb=" N GLY P 291 " --> pdb=" O VAL P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 293 through 299 Processing helix chain 'P' and resid 313 through 336 removed outlier: 4.982A pdb=" N ARG P 329 " --> pdb=" O GLU P 325 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'P' and resid 337 through 339 No H-bonds generated for 'chain 'P' and resid 337 through 339' Processing helix chain 'P' and resid 356 through 376 Processing helix chain 'P' and resid 381 through 393 Processing helix chain 'E' and resid 3 through 17 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.710A pdb=" N LEU E 28 " --> pdb=" O PRO E 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.804A pdb=" N PHE E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 61 Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.546A pdb=" N TYR E 76 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'Q' and resid 33 through 40 Processing helix chain 'Q' and resid 40 through 58 removed outlier: 4.928A pdb=" N ILE Q 50 " --> pdb=" O ILE Q 46 " (cutoff:3.500A) Proline residue: Q 51 - end of helix removed outlier: 3.779A pdb=" N ALA Q 57 " --> pdb=" O GLU Q 53 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY Q 58 " --> pdb=" O MET Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 78 removed outlier: 3.688A pdb=" N PHE Q 70 " --> pdb=" O ASP Q 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR Q 77 " --> pdb=" O LEU Q 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS Q 78 " --> pdb=" O TRP Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 94 Processing helix chain 'Q' and resid 127 through 129 No H-bonds generated for 'chain 'Q' and resid 127 through 129' Processing helix chain 'Q' and resid 176 through 183 removed outlier: 3.522A pdb=" N GLN Q 182 " --> pdb=" O GLN Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 215 removed outlier: 3.519A pdb=" N ILE Q 196 " --> pdb=" O ASN Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 250 removed outlier: 3.679A pdb=" N TYR Q 237 " --> pdb=" O ASP Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 274 through 291 removed outlier: 3.565A pdb=" N GLY Q 291 " --> pdb=" O VAL Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 299 Processing helix chain 'Q' and resid 309 through 336 removed outlier: 4.313A pdb=" N LEU Q 313 " --> pdb=" O GLN Q 309 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR Q 315 " --> pdb=" O THR Q 311 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE Q 316 " --> pdb=" O ALA Q 312 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ARG Q 329 " --> pdb=" O GLU Q 325 " (cutoff:3.500A) Proline residue: Q 330 - end of helix Processing helix chain 'Q' and resid 337 through 339 No H-bonds generated for 'chain 'Q' and resid 337 through 339' Processing helix chain 'Q' and resid 356 through 376 Processing helix chain 'Q' and resid 381 through 393 Processing helix chain 'F' and resid 3 through 17 Processing helix chain 'F' and resid 24 through 37 removed outlier: 3.720A pdb=" N LEU F 28 " --> pdb=" O PRO F 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 37 " --> pdb=" O GLU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 47 through 61 Processing helix chain 'F' and resid 72 through 76 removed outlier: 3.639A pdb=" N TYR F 76 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'R' and resid 33 through 40 Processing helix chain 'R' and resid 40 through 58 removed outlier: 4.919A pdb=" N ILE R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) Proline residue: R 51 - end of helix removed outlier: 3.735A pdb=" N ALA R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY R 58 " --> pdb=" O MET R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 78 removed outlier: 3.710A pdb=" N PHE R 70 " --> pdb=" O ASP R 66 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS R 78 " --> pdb=" O TRP R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 94 Processing helix chain 'R' and resid 127 through 129 No H-bonds generated for 'chain 'R' and resid 127 through 129' Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.550A pdb=" N GLN R 182 " --> pdb=" O GLN R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 215 Processing helix chain 'R' and resid 233 through 250 removed outlier: 3.646A pdb=" N TYR R 237 " --> pdb=" O ASP R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 291 removed outlier: 3.643A pdb=" N GLY R 291 " --> pdb=" O VAL R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 299 Processing helix chain 'R' and resid 313 through 336 removed outlier: 4.826A pdb=" N ARG R 329 " --> pdb=" O GLU R 325 " (cutoff:3.500A) Proline residue: R 330 - end of helix Processing helix chain 'R' and resid 337 through 339 No H-bonds generated for 'chain 'R' and resid 337 through 339' Processing helix chain 'R' and resid 356 through 376 Processing helix chain 'R' and resid 381 through 393 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.712A pdb=" N LEU G 28 " --> pdb=" O PRO G 24 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU G 37 " --> pdb=" O GLU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 46 No H-bonds generated for 'chain 'G' and resid 44 through 46' Processing helix chain 'G' and resid 47 through 61 Processing helix chain 'G' and resid 72 through 77 removed outlier: 3.556A pdb=" N TYR G 76 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'S' and resid 33 through 40 Processing helix chain 'S' and resid 40 through 58 removed outlier: 4.909A pdb=" N ILE S 50 " --> pdb=" O ILE S 46 " (cutoff:3.500A) Proline residue: S 51 - end of helix removed outlier: 3.693A pdb=" N ALA S 57 " --> pdb=" O GLU S 53 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY S 58 " --> pdb=" O MET S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 78 removed outlier: 3.704A pdb=" N PHE S 70 " --> pdb=" O ASP S 66 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR S 77 " --> pdb=" O LEU S 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS S 78 " --> pdb=" O TRP S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 94 Processing helix chain 'S' and resid 127 through 129 No H-bonds generated for 'chain 'S' and resid 127 through 129' Processing helix chain 'S' and resid 176 through 183 removed outlier: 3.564A pdb=" N GLN S 182 " --> pdb=" O GLN S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 215 Processing helix chain 'S' and resid 233 through 250 removed outlier: 3.686A pdb=" N TYR S 237 " --> pdb=" O ASP S 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 274 through 291 removed outlier: 3.610A pdb=" N GLY S 291 " --> pdb=" O VAL S 287 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 299 Processing helix chain 'S' and resid 313 through 336 removed outlier: 4.982A pdb=" N ARG S 329 " --> pdb=" O GLU S 325 " (cutoff:3.500A) Proline residue: S 330 - end of helix Processing helix chain 'S' and resid 337 through 339 No H-bonds generated for 'chain 'S' and resid 337 through 339' Processing helix chain 'S' and resid 356 through 376 Processing helix chain 'S' and resid 381 through 393 Processing helix chain 'H' and resid 3 through 17 Processing helix chain 'H' and resid 24 through 37 removed outlier: 3.714A pdb=" N LEU H 28 " --> pdb=" O PRO H 24 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU H 37 " --> pdb=" O GLU H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 46 No H-bonds generated for 'chain 'H' and resid 44 through 46' Processing helix chain 'H' and resid 47 through 61 Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 108 through 122 Processing helix chain 'T' and resid 33 through 40 Processing helix chain 'T' and resid 40 through 58 removed outlier: 4.927A pdb=" N ILE T 50 " --> pdb=" O ILE T 46 " (cutoff:3.500A) Proline residue: T 51 - end of helix removed outlier: 3.780A pdb=" N ALA T 57 " --> pdb=" O GLU T 53 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY T 58 " --> pdb=" O MET T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 78 removed outlier: 3.685A pdb=" N PHE T 70 " --> pdb=" O ASP T 66 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR T 77 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS T 78 " --> pdb=" O TRP T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 94 Processing helix chain 'T' and resid 127 through 129 No H-bonds generated for 'chain 'T' and resid 127 through 129' Processing helix chain 'T' and resid 176 through 183 removed outlier: 3.523A pdb=" N GLN T 182 " --> pdb=" O GLN T 178 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 215 removed outlier: 3.520A pdb=" N ILE T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) Processing helix chain 'T' and resid 233 through 250 removed outlier: 3.670A pdb=" N TYR T 237 " --> pdb=" O ASP T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 274 through 291 removed outlier: 3.563A pdb=" N GLY T 291 " --> pdb=" O VAL T 287 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 299 Processing helix chain 'T' and resid 309 through 336 removed outlier: 4.317A pdb=" N LEU T 313 " --> pdb=" O GLN T 309 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR T 315 " --> pdb=" O THR T 311 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N PHE T 316 " --> pdb=" O ALA T 312 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG T 329 " --> pdb=" O GLU T 325 " (cutoff:3.500A) Proline residue: T 330 - end of helix Processing helix chain 'T' and resid 337 through 339 No H-bonds generated for 'chain 'T' and resid 337 through 339' Processing helix chain 'T' and resid 356 through 376 Processing helix chain 'T' and resid 381 through 393 Processing helix chain 'I' and resid 3 through 17 Processing helix chain 'I' and resid 24 through 37 removed outlier: 3.727A pdb=" N LEU I 28 " --> pdb=" O PRO I 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU I 37 " --> pdb=" O GLU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 46 No H-bonds generated for 'chain 'I' and resid 44 through 46' Processing helix chain 'I' and resid 47 through 61 Processing helix chain 'I' and resid 72 through 76 removed outlier: 3.626A pdb=" N TYR I 76 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 122 Processing helix chain 'U' and resid 33 through 40 Processing helix chain 'U' and resid 40 through 58 removed outlier: 4.920A pdb=" N ILE U 50 " --> pdb=" O ILE U 46 " (cutoff:3.500A) Proline residue: U 51 - end of helix removed outlier: 3.736A pdb=" N ALA U 57 " --> pdb=" O GLU U 53 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY U 58 " --> pdb=" O MET U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 78 removed outlier: 3.704A pdb=" N PHE U 70 " --> pdb=" O ASP U 66 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR U 77 " --> pdb=" O LEU U 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS U 78 " --> pdb=" O TRP U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 94 Processing helix chain 'U' and resid 127 through 129 No H-bonds generated for 'chain 'U' and resid 127 through 129' Processing helix chain 'U' and resid 176 through 183 removed outlier: 3.547A pdb=" N GLN U 182 " --> pdb=" O GLN U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 192 through 215 Processing helix chain 'U' and resid 233 through 250 removed outlier: 3.648A pdb=" N TYR U 237 " --> pdb=" O ASP U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 274 through 291 removed outlier: 3.632A pdb=" N GLY U 291 " --> pdb=" O VAL U 287 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 299 Processing helix chain 'U' and resid 313 through 336 removed outlier: 4.764A pdb=" N ARG U 329 " --> pdb=" O GLU U 325 " (cutoff:3.500A) Proline residue: U 330 - end of helix Processing helix chain 'U' and resid 337 through 339 No H-bonds generated for 'chain 'U' and resid 337 through 339' Processing helix chain 'U' and resid 356 through 376 Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'J' and resid 3 through 17 Processing helix chain 'J' and resid 24 through 37 removed outlier: 3.708A pdb=" N LEU J 28 " --> pdb=" O PRO J 24 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU J 37 " --> pdb=" O GLU J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 46 No H-bonds generated for 'chain 'J' and resid 44 through 46' Processing helix chain 'J' and resid 47 through 61 Processing helix chain 'J' and resid 72 through 77 removed outlier: 3.576A pdb=" N TYR J 76 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 122 Processing helix chain 'V' and resid 33 through 40 Processing helix chain 'V' and resid 40 through 58 removed outlier: 4.908A pdb=" N ILE V 50 " --> pdb=" O ILE V 46 " (cutoff:3.500A) Proline residue: V 51 - end of helix removed outlier: 3.697A pdb=" N ALA V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY V 58 " --> pdb=" O MET V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 78 removed outlier: 3.684A pdb=" N PHE V 70 " --> pdb=" O ASP V 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR V 77 " --> pdb=" O LEU V 73 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS V 78 " --> pdb=" O TRP V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 94 Processing helix chain 'V' and resid 127 through 129 No H-bonds generated for 'chain 'V' and resid 127 through 129' Processing helix chain 'V' and resid 176 through 183 removed outlier: 3.563A pdb=" N GLN V 182 " --> pdb=" O GLN V 178 " (cutoff:3.500A) Processing helix chain 'V' and resid 192 through 215 Processing helix chain 'V' and resid 233 through 250 removed outlier: 3.641A pdb=" N TYR V 237 " --> pdb=" O ASP V 233 " (cutoff:3.500A) Processing helix chain 'V' and resid 274 through 291 removed outlier: 3.610A pdb=" N GLY V 291 " --> pdb=" O VAL V 287 " (cutoff:3.500A) Processing helix chain 'V' and resid 293 through 299 Processing helix chain 'V' and resid 313 through 336 removed outlier: 4.787A pdb=" N ARG V 329 " --> pdb=" O GLU V 325 " (cutoff:3.500A) Proline residue: V 330 - end of helix Processing helix chain 'V' and resid 337 through 339 No H-bonds generated for 'chain 'V' and resid 337 through 339' Processing helix chain 'V' and resid 356 through 376 Processing helix chain 'V' and resid 381 through 393 Processing helix chain 'K' and resid 3 through 17 Processing helix chain 'K' and resid 24 through 37 removed outlier: 3.714A pdb=" N LEU K 28 " --> pdb=" O PRO K 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU K 37 " --> pdb=" O GLU K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 46 No H-bonds generated for 'chain 'K' and resid 44 through 46' Processing helix chain 'K' and resid 47 through 61 Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 108 through 122 Processing helix chain 'W' and resid 33 through 40 Processing helix chain 'W' and resid 40 through 58 removed outlier: 4.925A pdb=" N ILE W 50 " --> pdb=" O ILE W 46 " (cutoff:3.500A) Proline residue: W 51 - end of helix removed outlier: 3.776A pdb=" N ALA W 57 " --> pdb=" O GLU W 53 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY W 58 " --> pdb=" O MET W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 78 removed outlier: 3.720A pdb=" N PHE W 70 " --> pdb=" O ASP W 66 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR W 77 " --> pdb=" O LEU W 73 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS W 78 " --> pdb=" O TRP W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 94 Processing helix chain 'W' and resid 127 through 129 No H-bonds generated for 'chain 'W' and resid 127 through 129' Processing helix chain 'W' and resid 176 through 183 removed outlier: 3.522A pdb=" N GLN W 182 " --> pdb=" O GLN W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 192 through 215 removed outlier: 3.522A pdb=" N ILE W 196 " --> pdb=" O ASN W 192 " (cutoff:3.500A) Processing helix chain 'W' and resid 233 through 250 removed outlier: 3.671A pdb=" N TYR W 237 " --> pdb=" O ASP W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 274 through 291 removed outlier: 3.563A pdb=" N GLY W 291 " --> pdb=" O VAL W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 299 Processing helix chain 'W' and resid 309 through 336 removed outlier: 4.339A pdb=" N LEU W 313 " --> pdb=" O GLN W 309 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR W 315 " --> pdb=" O THR W 311 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE W 316 " --> pdb=" O ALA W 312 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG W 329 " --> pdb=" O GLU W 325 " (cutoff:3.500A) Proline residue: W 330 - end of helix Processing helix chain 'W' and resid 337 through 339 No H-bonds generated for 'chain 'W' and resid 337 through 339' Processing helix chain 'W' and resid 356 through 376 Processing helix chain 'W' and resid 381 through 393 Processing helix chain 'L' and resid 3 through 17 Processing helix chain 'L' and resid 24 through 39 removed outlier: 3.758A pdb=" N LEU L 28 " --> pdb=" O PRO L 24 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU L 37 " --> pdb=" O GLU L 33 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE L 38 " --> pdb=" O MET L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 46 No H-bonds generated for 'chain 'L' and resid 44 through 46' Processing helix chain 'L' and resid 47 through 61 Processing helix chain 'L' and resid 72 through 76 removed outlier: 3.676A pdb=" N TYR L 76 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 122 Processing helix chain 'X' and resid 33 through 40 Processing helix chain 'X' and resid 40 through 58 removed outlier: 4.928A pdb=" N ILE X 50 " --> pdb=" O ILE X 46 " (cutoff:3.500A) Proline residue: X 51 - end of helix removed outlier: 3.746A pdb=" N ALA X 57 " --> pdb=" O GLU X 53 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY X 58 " --> pdb=" O MET X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 78 removed outlier: 3.659A pdb=" N PHE X 70 " --> pdb=" O ASP X 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR X 77 " --> pdb=" O LEU X 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS X 78 " --> pdb=" O TRP X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 94 Processing helix chain 'X' and resid 127 through 129 No H-bonds generated for 'chain 'X' and resid 127 through 129' Processing helix chain 'X' and resid 176 through 183 removed outlier: 3.549A pdb=" N GLN X 182 " --> pdb=" O GLN X 178 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 215 Processing helix chain 'X' and resid 233 through 250 removed outlier: 3.680A pdb=" N TYR X 237 " --> pdb=" O ASP X 233 " (cutoff:3.500A) Processing helix chain 'X' and resid 274 through 291 removed outlier: 3.648A pdb=" N GLY X 291 " --> pdb=" O VAL X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 293 through 299 Processing helix chain 'X' and resid 313 through 336 removed outlier: 4.767A pdb=" N ARG X 329 " --> pdb=" O GLU X 325 " (cutoff:3.500A) Proline residue: X 330 - end of helix Processing helix chain 'X' and resid 337 through 339 No H-bonds generated for 'chain 'X' and resid 337 through 339' Processing helix chain 'X' and resid 356 through 376 Processing helix chain 'X' and resid 381 through 393 Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 85 removed outlier: 5.859A pdb=" N THR B 81 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 82 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY B 94 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL A 80 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 13.007A pdb=" N ARG A 79 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N GLU A 95 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N THR A 81 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER L 82 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY A 94 " --> pdb=" O VAL L 80 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL L 80 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR L 81 " --> pdb=" O PHE L 93 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER K 82 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY L 94 " --> pdb=" O VAL K 80 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL K 80 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR K 81 " --> pdb=" O PHE K 93 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER J 82 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY K 94 " --> pdb=" O VAL J 80 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL J 80 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 13.066A pdb=" N ARG J 79 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N GLU J 95 " --> pdb=" O ARG J 79 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR J 81 " --> pdb=" O PHE J 93 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE J 89 " --> pdb=" O LEU J 85 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER I 82 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY J 94 " --> pdb=" O VAL I 80 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL I 80 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR I 81 " --> pdb=" O PHE I 93 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE I 89 " --> pdb=" O LEU I 85 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER H 82 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY I 94 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL H 80 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N THR H 81 " --> pdb=" O PHE H 93 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER G 82 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY H 94 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL G 80 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N ARG G 79 " --> pdb=" O GLU G 95 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLU G 95 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR G 81 " --> pdb=" O PHE G 93 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER F 82 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY G 94 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL F 80 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR F 81 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER E 82 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY F 94 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL E 80 " --> pdb=" O GLY F 94 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR E 81 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER D 82 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY E 94 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL D 80 " --> pdb=" O GLY E 94 " (cutoff:3.500A) removed outlier: 13.016A pdb=" N ARG D 79 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N GLU D 95 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR D 81 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER C 82 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY D 94 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL C 80 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N THR C 81 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 82 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY C 94 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B 80 " --> pdb=" O GLY C 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.592A pdb=" N MET B 128 " --> pdb=" O GLY O 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 59 through 62 Processing sheet with id=AA4, first strand: chain 'M' and resid 120 through 125 removed outlier: 3.611A pdb=" N GLY M 120 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA M 97 " --> pdb=" O TYR M 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 131 through 134 removed outlier: 6.873A pdb=" N ILE M 148 " --> pdb=" O GLU M 132 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG M 134 " --> pdb=" O PRO M 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 263 through 269 removed outlier: 3.535A pdb=" N LYS M 222 " --> pdb=" O GLU M 264 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ILE N 256 " --> pdb=" O GLN M 217 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ALA M 219 " --> pdb=" O ILE N 256 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE N 258 " --> pdb=" O ALA M 219 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TRP M 221 " --> pdb=" O ILE N 258 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET L 128 " --> pdb=" O GLY N 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA8, first strand: chain 'N' and resid 59 through 62 Processing sheet with id=AA9, first strand: chain 'N' and resid 120 through 125 removed outlier: 3.806A pdb=" N GLY N 120 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA N 97 " --> pdb=" O TYR N 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 131 through 134 removed outlier: 6.747A pdb=" N VAL N 131 " --> pdb=" O TYR N 149 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR N 149 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS N 133 " --> pdb=" O GLU N 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 263 through 269 removed outlier: 8.925A pdb=" N ILE X 256 " --> pdb=" O GLN N 217 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA N 219 " --> pdb=" O ILE X 256 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE X 258 " --> pdb=" O ALA N 219 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP N 221 " --> pdb=" O ILE X 258 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET K 128 " --> pdb=" O GLY X 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.566A pdb=" N MET C 128 " --> pdb=" O GLY P 257 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE P 256 " --> pdb=" O ALA Q 219 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS Q 222 " --> pdb=" O GLU Q 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 59 through 62 Processing sheet with id=AB5, first strand: chain 'O' and resid 120 through 125 removed outlier: 3.692A pdb=" N GLY O 120 " --> pdb=" O ILE O 101 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA O 97 " --> pdb=" O TYR O 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 131 through 134 removed outlier: 6.854A pdb=" N ILE O 148 " --> pdb=" O GLU O 132 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG O 134 " --> pdb=" O PRO O 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.517A pdb=" N MET D 128 " --> pdb=" O GLY Q 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 59 through 62 Processing sheet with id=AB9, first strand: chain 'P' and resid 120 through 125 removed outlier: 3.864A pdb=" N GLY P 120 " --> pdb=" O ILE P 101 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA P 97 " --> pdb=" O TYR P 124 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 131 through 134 removed outlier: 6.741A pdb=" N VAL P 131 " --> pdb=" O TYR P 149 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR P 149 " --> pdb=" O VAL P 131 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS P 133 " --> pdb=" O GLU P 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.598A pdb=" N MET E 128 " --> pdb=" O GLY R 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 59 through 62 Processing sheet with id=AC4, first strand: chain 'Q' and resid 120 through 125 removed outlier: 3.611A pdb=" N GLY Q 120 " --> pdb=" O ILE Q 101 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA Q 97 " --> pdb=" O TYR Q 124 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 131 through 134 removed outlier: 6.872A pdb=" N ILE Q 148 " --> pdb=" O GLU Q 132 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG Q 134 " --> pdb=" O PRO Q 146 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 128 through 129 removed outlier: 3.573A pdb=" N MET F 128 " --> pdb=" O GLY S 257 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE S 256 " --> pdb=" O ALA T 219 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS T 222 " --> pdb=" O GLU T 264 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 59 through 62 Processing sheet with id=AC8, first strand: chain 'R' and resid 120 through 125 removed outlier: 3.554A pdb=" N GLY R 120 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA R 97 " --> pdb=" O TYR R 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 131 through 134 removed outlier: 6.856A pdb=" N ILE R 148 " --> pdb=" O GLU R 132 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG R 134 " --> pdb=" O PRO R 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 128 through 129 removed outlier: 3.521A pdb=" N MET G 128 " --> pdb=" O GLY T 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 59 through 62 Processing sheet with id=AD3, first strand: chain 'S' and resid 120 through 125 removed outlier: 3.859A pdb=" N GLY S 120 " --> pdb=" O ILE S 101 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA S 97 " --> pdb=" O TYR S 124 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 131 through 134 removed outlier: 6.743A pdb=" N VAL S 131 " --> pdb=" O TYR S 149 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR S 149 " --> pdb=" O VAL S 131 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS S 133 " --> pdb=" O GLU S 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 128 through 129 removed outlier: 3.590A pdb=" N MET H 128 " --> pdb=" O GLY U 257 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 59 through 62 Processing sheet with id=AD7, first strand: chain 'T' and resid 120 through 125 removed outlier: 3.588A pdb=" N GLY T 120 " --> pdb=" O ILE T 101 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA T 97 " --> pdb=" O TYR T 124 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 131 through 134 removed outlier: 6.869A pdb=" N ILE T 148 " --> pdb=" O GLU T 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG T 134 " --> pdb=" O PRO T 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 128 through 129 removed outlier: 3.578A pdb=" N MET I 128 " --> pdb=" O GLY V 257 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS W 222 " --> pdb=" O GLU W 264 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 59 through 62 Processing sheet with id=AE2, first strand: chain 'U' and resid 120 through 125 removed outlier: 3.646A pdb=" N GLY U 120 " --> pdb=" O ILE U 101 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA U 97 " --> pdb=" O TYR U 124 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 131 through 134 removed outlier: 6.853A pdb=" N ILE U 148 " --> pdb=" O GLU U 132 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG U 134 " --> pdb=" O PRO U 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 128 through 129 removed outlier: 3.511A pdb=" N MET J 128 " --> pdb=" O GLY W 257 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 59 through 62 Processing sheet with id=AE6, first strand: chain 'V' and resid 120 through 125 removed outlier: 3.832A pdb=" N GLY V 120 " --> pdb=" O ILE V 101 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA V 97 " --> pdb=" O TYR V 124 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 131 through 134 removed outlier: 6.749A pdb=" N VAL V 131 " --> pdb=" O TYR V 149 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR V 149 " --> pdb=" O VAL V 131 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS V 133 " --> pdb=" O GLU V 147 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 59 through 62 Processing sheet with id=AE9, first strand: chain 'W' and resid 120 through 125 removed outlier: 3.614A pdb=" N GLY W 120 " --> pdb=" O ILE W 101 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA W 97 " --> pdb=" O TYR W 124 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 131 through 134 removed outlier: 6.864A pdb=" N ILE W 148 " --> pdb=" O GLU W 132 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG W 134 " --> pdb=" O PRO W 146 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 59 through 62 Processing sheet with id=AF3, first strand: chain 'X' and resid 120 through 125 removed outlier: 3.525A pdb=" N GLY X 120 " --> pdb=" O ILE X 101 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA X 97 " --> pdb=" O TYR X 124 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 131 through 134 removed outlier: 6.856A pdb=" N ILE X 148 " --> pdb=" O GLU X 132 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ARG X 134 " --> pdb=" O PRO X 146 " (cutoff:3.500A) 2400 hydrogen bonds defined for protein. 7056 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: 10.49 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16011 1.34 - 1.46: 6433 1.46 - 1.58: 26000 1.58 - 1.69: 0 1.69 - 1.81: 372 Bond restraints: 48816 Sorted by residual: bond pdb=" CB GLN A 41 " pdb=" CG GLN A 41 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.34e+00 bond pdb=" CB GLN H 41 " pdb=" CG GLN H 41 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CB GLN B 41 " pdb=" CG GLN B 41 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CA CYS U 230 " pdb=" C CYS U 230 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.38e-02 5.25e+03 1.88e+00 bond pdb=" CA CYS R 230 " pdb=" C CYS R 230 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.38e-02 5.25e+03 1.72e+00 ... (remaining 48811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 64472 1.61 - 3.22: 1166 3.22 - 4.83: 161 4.83 - 6.44: 38 6.44 - 8.05: 7 Bond angle restraints: 65844 Sorted by residual: angle pdb=" CA GLN A 41 " pdb=" CB GLN A 41 " pdb=" CG GLN A 41 " ideal model delta sigma weight residual 114.10 122.15 -8.05 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CA GLN H 41 " pdb=" CB GLN H 41 " pdb=" CG GLN H 41 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CA GLN B 41 " pdb=" CB GLN B 41 " pdb=" CG GLN B 41 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CB GLN A 41 " pdb=" CG GLN A 41 " pdb=" CD GLN A 41 " ideal model delta sigma weight residual 112.60 118.61 -6.01 1.70e+00 3.46e-01 1.25e+01 angle pdb=" CB GLN H 41 " pdb=" CG GLN H 41 " pdb=" CD GLN H 41 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.70e+00 3.46e-01 1.22e+01 ... (remaining 65839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 26072 17.44 - 34.89: 2823 34.89 - 52.33: 813 52.33 - 69.77: 127 69.77 - 87.22: 21 Dihedral angle restraints: 29856 sinusoidal: 12228 harmonic: 17628 Sorted by residual: dihedral pdb=" CA ASP T 266 " pdb=" CB ASP T 266 " pdb=" CG ASP T 266 " pdb=" OD1 ASP T 266 " ideal model delta sinusoidal sigma weight residual -30.00 -89.19 59.19 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP W 266 " pdb=" CB ASP W 266 " pdb=" CG ASP W 266 " pdb=" OD1 ASP W 266 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP M 266 " pdb=" CB ASP M 266 " pdb=" CG ASP M 266 " pdb=" OD1 ASP M 266 " ideal model delta sinusoidal sigma weight residual -30.00 -89.13 59.13 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 29853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4595 0.027 - 0.053: 1663 0.053 - 0.080: 555 0.080 - 0.106: 314 0.106 - 0.133: 169 Chirality restraints: 7296 Sorted by residual: chirality pdb=" CA GLU X 377 " pdb=" N GLU X 377 " pdb=" C GLU X 377 " pdb=" CB GLU X 377 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE O 101 " pdb=" N ILE O 101 " pdb=" C ILE O 101 " pdb=" CB ILE O 101 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE U 101 " pdb=" N ILE U 101 " pdb=" C ILE U 101 " pdb=" CB ILE U 101 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 7293 not shown) Planarity restraints: 8544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 393 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO N 394 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO N 394 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 394 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA V 393 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO V 394 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO V 394 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO V 394 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA P 393 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO P 394 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO P 394 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO P 394 " 0.035 5.00e-02 4.00e+02 ... (remaining 8541 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 13705 2.82 - 3.34: 44426 3.34 - 3.86: 73096 3.86 - 4.38: 80675 4.38 - 4.90: 147518 Nonbonded interactions: 359420 Sorted by model distance: nonbonded pdb=" N GLU V 67 " pdb=" OE1 GLU V 67 " model vdw 2.296 3.120 nonbonded pdb=" NE1 TRP W 221 " pdb=" OE2 GLU W 263 " model vdw 2.301 3.120 nonbonded pdb=" NE1 TRP M 221 " pdb=" OE2 GLU M 263 " model vdw 2.305 3.120 nonbonded pdb=" NE1 TRP P 221 " pdb=" OE2 GLU P 263 " model vdw 2.306 3.120 nonbonded pdb=" NZ LYS R 222 " pdb=" OD2 ASP R 266 " model vdw 2.308 3.120 ... (remaining 359415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.610 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 : 0.002 0.059 48816 Z= 0.122 Angle : 0.540 8.053 65844 Z= 0.301 Chirality : 0.038 0.133 7296 Planarity : 0.004 0.067 8544 Dihedral : 15.593 87.215 18456 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.83 % Allowed : 4.77 % Favored : 94.40 % Rotamer: Outliers : 0.27 % Allowed : 19.90 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.11), residues: 6000 helix: 2.50 (0.10), residues: 2916 sheet: -1.74 (0.20), residues: 636 loop : -1.64 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 324 TYR 0.008 0.001 TYR M 37 PHE 0.012 0.001 PHE R 338 TRP 0.008 0.001 TRP W 89 HIS 0.003 0.001 HIS I 58 Details of bonding type rmsd covalent geometry : bond 0.00241 (48816) covalent geometry : angle 0.53986 (65844) hydrogen bonds : bond 0.15798 ( 2400) hydrogen bonds : angle 6.23677 ( 7056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1758 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1744 time to evaluate : 1.577 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 11 GLU cc_start: 0.6864 (tp30) cc_final: 0.6214 (tp30) REVERT: N 236 GLN cc_start: 0.7595 (mt0) cc_final: 0.7388 (mt0) REVERT: C 11 GLU cc_start: 0.7057 (tp30) cc_final: 0.6808 (tp30) REVERT: O 236 GLN cc_start: 0.7497 (mt0) cc_final: 0.7081 (mt0) REVERT: O 357 LYS cc_start: 0.6934 (mtmt) cc_final: 0.6516 (mtpp) REVERT: E 11 GLU cc_start: 0.6560 (tp30) cc_final: 0.5618 (tp30) REVERT: F 11 GLU cc_start: 0.7084 (tp30) cc_final: 0.6790 (tp30) REVERT: F 78 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6798 (tmm-80) REVERT: R 236 GLN cc_start: 0.7460 (mt0) cc_final: 0.7007 (mt0) REVERT: R 357 LYS cc_start: 0.6916 (mtmt) cc_final: 0.6502 (mtpp) REVERT: G 11 GLU cc_start: 0.6709 (tp30) cc_final: 0.6082 (tp30) REVERT: H 11 GLU cc_start: 0.6427 (tp30) cc_final: 0.5421 (tp30) REVERT: I 11 GLU cc_start: 0.7046 (tp30) cc_final: 0.6690 (tp30) REVERT: U 236 GLN cc_start: 0.7447 (mt0) cc_final: 0.7008 (mt0) REVERT: U 357 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6592 (mtpp) REVERT: J 11 GLU cc_start: 0.6676 (tp30) cc_final: 0.6118 (tp30) REVERT: K 11 GLU cc_start: 0.6442 (tp30) cc_final: 0.5460 (tp30) REVERT: L 11 GLU cc_start: 0.7075 (tp30) cc_final: 0.6802 (tp30) REVERT: X 236 GLN cc_start: 0.7439 (mt0) cc_final: 0.7114 (mt0) REVERT: X 357 LYS cc_start: 0.7087 (mtmt) cc_final: 0.6624 (mtpp) outliers start: 14 outliers final: 1 residues processed: 1748 average time/residue: 0.2746 time to fit residues: 770.3483 Evaluate side-chains 1258 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1257 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 84 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 597 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 182 GLN M 211 GLN M 217 GLN M 299 ASN O 178 GLN O 245 GLN D 91 GLN E 41 GLN Q 182 GLN Q 211 GLN Q 217 GLN R 178 GLN R 245 GLN ** R 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 182 GLN T 211 GLN T 217 GLN U 178 GLN U 245 GLN J 91 GLN W 217 GLN W 299 ASN X 245 GLN ** X 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.063963 restraints weight = 117080.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.066320 restraints weight = 60745.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.067892 restraints weight = 40160.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.068914 restraints weight = 30706.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.069552 restraints weight = 25785.472| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 48816 Z= 0.216 Angle : 0.632 7.711 65844 Z= 0.339 Chirality : 0.042 0.153 7296 Planarity : 0.004 0.046 8544 Dihedral : 3.933 16.356 6589 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.80 % Allowed : 5.72 % Favored : 93.48 % Rotamer: Outliers : 2.44 % Allowed : 20.75 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.11), residues: 6000 helix: 2.64 (0.10), residues: 2940 sheet: -1.24 (0.22), residues: 612 loop : -1.51 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 180 TYR 0.015 0.001 TYR X 265 PHE 0.020 0.002 PHE D 83 TRP 0.009 0.001 TRP M 221 HIS 0.004 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00501 (48816) covalent geometry : angle 0.63249 (65844) hydrogen bonds : bond 0.05400 ( 2400) hydrogen bonds : angle 4.88146 ( 7056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 1184 time to evaluate : 2.038 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: B 15 LYS cc_start: 0.9117 (mtmm) cc_final: 0.8121 (mtmm) REVERT: B 33 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8679 (mt-10) REVERT: B 71 GLU cc_start: 0.8094 (mp0) cc_final: 0.7761 (mp0) REVERT: M 61 MET cc_start: 0.8106 (ptp) cc_final: 0.7895 (ptp) REVERT: M 301 ASN cc_start: 0.8507 (t0) cc_final: 0.8286 (t0) REVERT: M 314 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 33 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8563 (mt-10) REVERT: A 71 GLU cc_start: 0.8259 (mp0) cc_final: 0.7833 (mp0) REVERT: A 82 SER cc_start: 0.9372 (p) cc_final: 0.9152 (p) REVERT: A 104 MET cc_start: 0.8580 (ttp) cc_final: 0.8176 (ttp) REVERT: A 105 MET cc_start: 0.8405 (mmm) cc_final: 0.8172 (mmm) REVERT: N 145 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8237 (mp0) REVERT: N 182 GLN cc_start: 0.8567 (mt0) cc_final: 0.8305 (mp10) REVERT: N 261 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: N 362 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8614 (mt-10) REVERT: C 71 GLU cc_start: 0.8134 (mp0) cc_final: 0.7568 (mp0) REVERT: C 74 GLU cc_start: 0.8608 (tp30) cc_final: 0.8146 (tp30) REVERT: O 157 MET cc_start: 0.8870 (mpp) cc_final: 0.8551 (mpp) REVERT: O 182 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: O 357 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8535 (mtmm) REVERT: D 11 GLU cc_start: 0.9330 (tp30) cc_final: 0.8972 (tp30) REVERT: D 71 GLU cc_start: 0.8232 (mp0) cc_final: 0.7800 (mp0) REVERT: D 82 SER cc_start: 0.9391 (p) cc_final: 0.9169 (p) REVERT: D 104 MET cc_start: 0.8485 (ttp) cc_final: 0.7998 (ttp) REVERT: D 105 MET cc_start: 0.8380 (mmm) cc_final: 0.8177 (mmm) REVERT: P 79 LEU cc_start: 0.9323 (mt) cc_final: 0.9075 (mt) REVERT: P 111 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8186 (tm-30) REVERT: P 145 GLU cc_start: 0.8516 (mp0) cc_final: 0.8012 (mp0) REVERT: P 182 GLN cc_start: 0.8570 (mt0) cc_final: 0.8306 (mp10) REVERT: P 362 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8552 (mt-10) REVERT: P 398 LEU cc_start: 0.9116 (tp) cc_final: 0.8910 (tp) REVERT: E 15 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8088 (mtmm) REVERT: E 33 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8698 (mt-10) REVERT: E 71 GLU cc_start: 0.8136 (mp0) cc_final: 0.7811 (mp0) REVERT: Q 145 GLU cc_start: 0.8497 (mp0) cc_final: 0.8190 (mp0) REVERT: Q 301 ASN cc_start: 0.8486 (t0) cc_final: 0.8262 (t0) REVERT: Q 314 GLU cc_start: 0.8229 (mm-30) cc_final: 0.8007 (mm-30) REVERT: F 71 GLU cc_start: 0.8149 (mp0) cc_final: 0.7723 (mp0) REVERT: F 74 GLU cc_start: 0.8707 (tp30) cc_final: 0.8193 (tp30) REVERT: F 78 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7992 (ptt90) REVERT: R 182 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8314 (mp10) REVERT: R 357 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8473 (mtmm) REVERT: G 11 GLU cc_start: 0.9256 (tp30) cc_final: 0.9041 (tp30) REVERT: G 33 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8598 (mt-10) REVERT: G 71 GLU cc_start: 0.8236 (mp0) cc_final: 0.7800 (mp0) REVERT: G 104 MET cc_start: 0.8421 (ttp) cc_final: 0.7898 (ttp) REVERT: S 65 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8677 (ptpp) REVERT: S 111 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8190 (tm-30) REVERT: S 145 GLU cc_start: 0.8679 (mp0) cc_final: 0.8202 (mp0) REVERT: S 182 GLN cc_start: 0.8605 (mt0) cc_final: 0.8330 (mp10) REVERT: S 228 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8512 (mp0) REVERT: S 261 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: S 398 LEU cc_start: 0.8905 (tp) cc_final: 0.8671 (tp) REVERT: H 15 LYS cc_start: 0.9013 (mtmm) cc_final: 0.8005 (mtmm) REVERT: H 33 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8694 (mt-10) REVERT: H 69 GLU cc_start: 0.8623 (tp30) cc_final: 0.8384 (tp30) REVERT: H 71 GLU cc_start: 0.8130 (mp0) cc_final: 0.7844 (mp0) REVERT: T 145 GLU cc_start: 0.8484 (mp0) cc_final: 0.8151 (mp0) REVERT: T 301 ASN cc_start: 0.8572 (t0) cc_final: 0.8357 (t0) REVERT: I 33 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8693 (mt-10) REVERT: I 71 GLU cc_start: 0.8156 (mp0) cc_final: 0.7634 (mp0) REVERT: I 74 GLU cc_start: 0.8658 (tp30) cc_final: 0.8152 (tp30) REVERT: U 54 MET cc_start: 0.8772 (mtm) cc_final: 0.8560 (mtm) REVERT: U 182 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: U 357 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8485 (mtmm) REVERT: J 11 GLU cc_start: 0.9290 (tp30) cc_final: 0.9024 (tp30) REVERT: J 71 GLU cc_start: 0.8237 (mp0) cc_final: 0.7798 (mp0) REVERT: J 82 SER cc_start: 0.9405 (p) cc_final: 0.9181 (p) REVERT: J 104 MET cc_start: 0.8422 (ttp) cc_final: 0.7922 (ttp) REVERT: J 105 MET cc_start: 0.8407 (mmm) cc_final: 0.8202 (mmm) REVERT: V 111 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8157 (tm-30) REVERT: V 145 GLU cc_start: 0.8981 (mp0) cc_final: 0.8305 (mp0) REVERT: V 182 GLN cc_start: 0.8588 (mt0) cc_final: 0.8328 (mp10) REVERT: V 261 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: K 15 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8015 (mtmm) REVERT: K 33 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8674 (mt-10) REVERT: K 71 GLU cc_start: 0.8126 (mp0) cc_final: 0.7773 (mp0) REVERT: W 145 GLU cc_start: 0.8556 (mp0) cc_final: 0.8292 (mp0) REVERT: W 301 ASN cc_start: 0.8592 (t0) cc_final: 0.8373 (t0) REVERT: W 314 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7895 (mm-30) REVERT: L 33 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8613 (mt-10) REVERT: L 71 GLU cc_start: 0.8177 (mp0) cc_final: 0.7719 (mp0) REVERT: L 74 GLU cc_start: 0.8565 (tp30) cc_final: 0.8128 (tp30) REVERT: X 54 MET cc_start: 0.8750 (mtm) cc_final: 0.8538 (mtm) REVERT: X 157 MET cc_start: 0.8870 (mpp) cc_final: 0.8548 (mpp) REVERT: X 357 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8458 (mtmm) outliers start: 127 outliers final: 69 residues processed: 1271 average time/residue: 0.2847 time to fit residues: 594.3496 Evaluate side-chains 1151 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1075 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 357 LYS Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 182 GLN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 229 MET Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain Q residue 357 LYS Chi-restraints excluded: chain Q residue 375 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 182 GLN Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain S residue 42 THR Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 357 LYS Chi-restraints excluded: chain T residue 375 ILE Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 128 MET Chi-restraints excluded: chain U residue 182 GLN Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain V residue 42 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 311 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 357 LYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain X residue 178 GLN Chi-restraints excluded: chain X residue 375 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 598 optimal weight: 3.9990 chunk 438 optimal weight: 4.9990 chunk 422 optimal weight: 4.9990 chunk 70 optimal weight: 0.0040 chunk 247 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 305 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 589 optimal weight: 0.6980 chunk 597 optimal weight: 1.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 182 GLN P 217 GLN Q 182 GLN S 217 GLN T 182 GLN V 217 GLN V 402 ASN W 182 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.089975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.066359 restraints weight = 115553.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.068762 restraints weight = 59049.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.070371 restraints weight = 38819.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.071440 restraints weight = 29602.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.072133 restraints weight = 24809.233| |-----------------------------------------------------------------------------| r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 48816 Z= 0.119 Angle : 0.554 7.626 65844 Z= 0.296 Chirality : 0.040 0.140 7296 Planarity : 0.003 0.038 8544 Dihedral : 3.748 13.594 6588 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.80 % Allowed : 4.12 % Favored : 95.08 % Rotamer: Outliers : 2.52 % Allowed : 21.86 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.11), residues: 6000 helix: 2.77 (0.10), residues: 2952 sheet: -0.87 (0.22), residues: 588 loop : -1.46 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 142 TYR 0.009 0.001 TYR B 55 PHE 0.022 0.001 PHE H 83 TRP 0.007 0.001 TRP Q 89 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00266 (48816) covalent geometry : angle 0.55436 (65844) hydrogen bonds : bond 0.03873 ( 2400) hydrogen bonds : angle 4.39768 ( 7056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1174 time to evaluate : 1.208 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: B 15 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8187 (mtmm) REVERT: B 33 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8493 (mt-10) REVERT: B 71 GLU cc_start: 0.8141 (mp0) cc_final: 0.7831 (mp0) REVERT: M 301 ASN cc_start: 0.8146 (t0) cc_final: 0.7912 (t0) REVERT: M 314 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7929 (mm-30) REVERT: M 398 LEU cc_start: 0.8794 (tp) cc_final: 0.8544 (tp) REVERT: A 11 GLU cc_start: 0.9234 (tp30) cc_final: 0.8775 (tp30) REVERT: A 33 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8467 (mt-10) REVERT: A 71 GLU cc_start: 0.8404 (mp0) cc_final: 0.7961 (mp0) REVERT: A 82 SER cc_start: 0.9240 (p) cc_final: 0.9029 (p) REVERT: A 104 MET cc_start: 0.8445 (ttp) cc_final: 0.8146 (ttp) REVERT: A 105 MET cc_start: 0.8298 (mmm) cc_final: 0.8088 (mmm) REVERT: N 145 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8294 (mp0) REVERT: N 236 GLN cc_start: 0.8857 (mt0) cc_final: 0.8565 (tt0) REVERT: N 261 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8215 (pt0) REVERT: N 362 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8766 (mt-10) REVERT: N 378 GLN cc_start: 0.9058 (mp10) cc_final: 0.8839 (pm20) REVERT: C 71 GLU cc_start: 0.8290 (mp0) cc_final: 0.7740 (mp0) REVERT: C 74 GLU cc_start: 0.8573 (tp30) cc_final: 0.7970 (tp30) REVERT: C 98 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8374 (mmtp) REVERT: O 157 MET cc_start: 0.8828 (mpp) cc_final: 0.8426 (mpp) REVERT: O 326 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7210 (tm-30) REVERT: D 11 GLU cc_start: 0.9277 (tp30) cc_final: 0.8846 (tp30) REVERT: D 33 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8560 (mt-10) REVERT: D 71 GLU cc_start: 0.8384 (mp0) cc_final: 0.7916 (mp0) REVERT: D 82 SER cc_start: 0.9269 (p) cc_final: 0.9060 (p) REVERT: D 104 MET cc_start: 0.8324 (ttp) cc_final: 0.7887 (ttp) REVERT: P 111 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8265 (tm-30) REVERT: P 145 GLU cc_start: 0.8528 (mp0) cc_final: 0.7897 (mp0) REVERT: P 261 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8312 (pt0) REVERT: P 362 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8739 (mt-10) REVERT: P 398 LEU cc_start: 0.9162 (tp) cc_final: 0.8941 (tp) REVERT: E 15 LYS cc_start: 0.8877 (mtmm) cc_final: 0.7812 (mtmm) REVERT: E 33 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8484 (mt-10) REVERT: E 71 GLU cc_start: 0.7999 (mp0) cc_final: 0.7736 (mp0) REVERT: Q 60 LYS cc_start: 0.8524 (ptpp) cc_final: 0.8109 (ptpp) REVERT: Q 132 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8623 (mm-30) REVERT: Q 301 ASN cc_start: 0.8091 (t0) cc_final: 0.7884 (t0) REVERT: Q 314 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7939 (mm-30) REVERT: Q 398 LEU cc_start: 0.8804 (tp) cc_final: 0.8550 (tp) REVERT: F 71 GLU cc_start: 0.8296 (mp0) cc_final: 0.7716 (mp0) REVERT: F 74 GLU cc_start: 0.8681 (tp30) cc_final: 0.8153 (tp30) REVERT: F 78 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7987 (ptt90) REVERT: F 98 LYS cc_start: 0.8671 (mmtp) cc_final: 0.8450 (mmtp) REVERT: R 68 LYS cc_start: 0.9271 (tppt) cc_final: 0.9034 (tppt) REVERT: R 157 MET cc_start: 0.8849 (mpp) cc_final: 0.8550 (mpp) REVERT: R 230 CYS cc_start: 0.8513 (m) cc_final: 0.8210 (t) REVERT: G 33 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8517 (mt-10) REVERT: G 71 GLU cc_start: 0.8425 (mp0) cc_final: 0.8045 (mp0) REVERT: G 104 MET cc_start: 0.8365 (ttp) cc_final: 0.8050 (ttp) REVERT: S 145 GLU cc_start: 0.8667 (mp0) cc_final: 0.8303 (mp0) REVERT: S 261 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: S 398 LEU cc_start: 0.8828 (tp) cc_final: 0.8528 (tp) REVERT: H 15 LYS cc_start: 0.8871 (mtmm) cc_final: 0.7770 (mtmm) REVERT: H 33 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8463 (mt-10) REVERT: H 71 GLU cc_start: 0.8208 (mp0) cc_final: 0.7900 (mp0) REVERT: T 301 ASN cc_start: 0.8084 (t0) cc_final: 0.7864 (t0) REVERT: T 398 LEU cc_start: 0.8785 (tp) cc_final: 0.8536 (tp) REVERT: I 33 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8621 (mt-10) REVERT: I 71 GLU cc_start: 0.8403 (mp0) cc_final: 0.8032 (mp0) REVERT: I 74 GLU cc_start: 0.8665 (tp30) cc_final: 0.8062 (tp30) REVERT: I 98 LYS cc_start: 0.8651 (mmtp) cc_final: 0.8392 (mmtp) REVERT: U 157 MET cc_start: 0.8840 (mpp) cc_final: 0.8481 (mpp) REVERT: U 230 CYS cc_start: 0.8521 (m) cc_final: 0.8225 (t) REVERT: J 71 GLU cc_start: 0.8418 (mp0) cc_final: 0.7979 (mp0) REVERT: J 82 SER cc_start: 0.9264 (p) cc_final: 0.9056 (p) REVERT: J 104 MET cc_start: 0.8361 (ttp) cc_final: 0.7943 (ttp) REVERT: J 105 MET cc_start: 0.8275 (mmm) cc_final: 0.8062 (mmm) REVERT: V 111 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8269 (tm-30) REVERT: V 145 GLU cc_start: 0.8956 (mp0) cc_final: 0.8244 (mp0) REVERT: V 224 LYS cc_start: 0.9148 (tptt) cc_final: 0.8912 (tptt) REVERT: V 261 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8331 (pt0) REVERT: V 323 LYS cc_start: 0.9416 (mmtt) cc_final: 0.9133 (mmmt) REVERT: K 15 LYS cc_start: 0.8869 (mtmm) cc_final: 0.7792 (mtmm) REVERT: K 33 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8479 (mt-10) REVERT: K 71 GLU cc_start: 0.8072 (mp0) cc_final: 0.7754 (mp0) REVERT: W 301 ASN cc_start: 0.8220 (t0) cc_final: 0.7981 (t0) REVERT: W 398 LEU cc_start: 0.8787 (tp) cc_final: 0.8532 (tp) REVERT: L 33 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8591 (mt-10) REVERT: L 71 GLU cc_start: 0.8400 (mp0) cc_final: 0.8047 (mp0) REVERT: L 74 GLU cc_start: 0.8564 (tp30) cc_final: 0.8148 (tp30) REVERT: L 98 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8429 (mmtp) REVERT: X 157 MET cc_start: 0.8817 (mpp) cc_final: 0.8423 (mpp) outliers start: 131 outliers final: 58 residues processed: 1262 average time/residue: 0.2285 time to fit residues: 473.9147 Evaluate side-chains 1140 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 1077 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain O residue 65 LYS Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 375 ILE Chi-restraints excluded: chain O residue 395 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain P residue 261 GLU Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain P residue 375 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain R residue 375 ILE Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain S residue 375 ILE Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 272 ILE Chi-restraints excluded: chain V residue 275 VAL Chi-restraints excluded: chain V residue 375 ILE Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 294 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 118 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 chunk 409 optimal weight: 7.9990 chunk 336 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 498 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 182 GLN O 177 GLN O 299 ASN Q 299 ASN R 177 GLN R 299 ASN T 299 ASN U 177 GLN U 299 ASN J 91 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.085483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.062599 restraints weight = 118174.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.065077 restraints weight = 58896.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.066707 restraints weight = 38033.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.067763 restraints weight = 28698.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.068446 restraints weight = 23989.015| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48816 Z= 0.144 Angle : 0.549 6.325 65844 Z= 0.294 Chirality : 0.040 0.132 7296 Planarity : 0.003 0.033 8544 Dihedral : 3.736 13.644 6588 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.80 % Allowed : 4.83 % Favored : 94.37 % Rotamer: Outliers : 3.19 % Allowed : 22.04 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.11), residues: 6000 helix: 3.04 (0.10), residues: 2868 sheet: -0.94 (0.22), residues: 588 loop : -1.38 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 78 TYR 0.008 0.001 TYR K 55 PHE 0.009 0.001 PHE V 70 TRP 0.007 0.001 TRP Q 89 HIS 0.003 0.000 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00332 (48816) covalent geometry : angle 0.54904 (65844) hydrogen bonds : bond 0.04150 ( 2400) hydrogen bonds : angle 4.27621 ( 7056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1094 time to evaluate : 1.637 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: B 33 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 69 GLU cc_start: 0.7735 (pp20) cc_final: 0.6484 (pp20) REVERT: B 71 GLU cc_start: 0.8196 (mp0) cc_final: 0.7788 (mp0) REVERT: A 71 GLU cc_start: 0.8466 (mp0) cc_final: 0.8019 (mp0) REVERT: A 82 SER cc_start: 0.9218 (p) cc_final: 0.9017 (p) REVERT: A 104 MET cc_start: 0.8506 (ttp) cc_final: 0.8161 (ttp) REVERT: N 145 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8331 (mp0) REVERT: N 184 GLN cc_start: 0.8289 (mp10) cc_final: 0.7998 (mp10) REVERT: N 261 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: N 362 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8731 (mt-10) REVERT: C 71 GLU cc_start: 0.8458 (mp0) cc_final: 0.7930 (mp0) REVERT: C 74 GLU cc_start: 0.8453 (tp30) cc_final: 0.8075 (tp30) REVERT: C 98 LYS cc_start: 0.8648 (mmtp) cc_final: 0.8423 (mmtp) REVERT: C 104 MET cc_start: 0.8606 (ttt) cc_final: 0.8382 (ttt) REVERT: O 54 MET cc_start: 0.8839 (mtm) cc_final: 0.8574 (mtm) REVERT: O 157 MET cc_start: 0.8861 (mpp) cc_final: 0.8452 (mpp) REVERT: O 357 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8073 (mmmm) REVERT: O 360 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7829 (mt-10) REVERT: O 400 ASP cc_start: 0.8586 (t0) cc_final: 0.8337 (t0) REVERT: D 11 GLU cc_start: 0.9192 (tp30) cc_final: 0.8963 (tp30) REVERT: D 33 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8405 (mt-10) REVERT: D 71 GLU cc_start: 0.8439 (mp0) cc_final: 0.7977 (mp0) REVERT: D 82 SER cc_start: 0.9238 (p) cc_final: 0.9028 (p) REVERT: P 68 LYS cc_start: 0.9327 (tppt) cc_final: 0.9002 (tppt) REVERT: P 145 GLU cc_start: 0.8514 (mp0) cc_final: 0.7920 (mp0) REVERT: P 184 GLN cc_start: 0.8292 (mp10) cc_final: 0.7994 (mp10) REVERT: P 203 ASP cc_start: 0.8920 (m-30) cc_final: 0.8718 (m-30) REVERT: P 261 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: P 362 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8662 (mt-10) REVERT: P 398 LEU cc_start: 0.9128 (tp) cc_final: 0.8907 (tp) REVERT: E 15 LYS cc_start: 0.9035 (mtmm) cc_final: 0.7991 (mtmm) REVERT: E 33 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8384 (mt-10) REVERT: E 69 GLU cc_start: 0.7750 (pp20) cc_final: 0.6529 (pp20) REVERT: E 71 GLU cc_start: 0.8109 (mp0) cc_final: 0.7810 (mp0) REVERT: Q 132 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8622 (mm-30) REVERT: Q 183 ASN cc_start: 0.9047 (t0) cc_final: 0.8685 (t0) REVERT: Q 314 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7879 (mm-30) REVERT: F 6 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8852 (mp) REVERT: F 71 GLU cc_start: 0.8490 (mp0) cc_final: 0.7965 (mp0) REVERT: F 74 GLU cc_start: 0.8699 (tp30) cc_final: 0.8157 (tp30) REVERT: F 78 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8035 (ptt90) REVERT: F 98 LYS cc_start: 0.8670 (mmtp) cc_final: 0.8460 (mmtp) REVERT: F 104 MET cc_start: 0.8617 (ttt) cc_final: 0.8396 (ttt) REVERT: F 120 ARG cc_start: 0.8788 (mtp85) cc_final: 0.8512 (tpt-90) REVERT: R 157 MET cc_start: 0.8880 (mpp) cc_final: 0.8500 (mpp) REVERT: R 326 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7534 (tm-30) REVERT: G 33 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8567 (mt-10) REVERT: G 71 GLU cc_start: 0.8453 (mp0) cc_final: 0.7934 (mp0) REVERT: S 68 LYS cc_start: 0.9251 (tppt) cc_final: 0.8925 (tppt) REVERT: S 145 GLU cc_start: 0.8683 (mp0) cc_final: 0.8278 (mp0) REVERT: S 157 MET cc_start: 0.8769 (mpp) cc_final: 0.8427 (mpp) REVERT: S 184 GLN cc_start: 0.8322 (mp10) cc_final: 0.8023 (mp10) REVERT: S 261 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8255 (pt0) REVERT: H 15 LYS cc_start: 0.9048 (mtmm) cc_final: 0.7997 (mtmm) REVERT: H 33 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8367 (mt-10) REVERT: H 71 GLU cc_start: 0.8149 (mp0) cc_final: 0.7885 (mp0) REVERT: T 79 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8986 (mp) REVERT: T 183 ASN cc_start: 0.9037 (t0) cc_final: 0.8677 (t0) REVERT: I 33 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8532 (mt-10) REVERT: I 71 GLU cc_start: 0.8688 (mp0) cc_final: 0.8208 (mp0) REVERT: I 74 GLU cc_start: 0.8513 (tp30) cc_final: 0.7965 (tp30) REVERT: I 98 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8441 (mmtp) REVERT: I 104 MET cc_start: 0.8621 (ttt) cc_final: 0.8405 (ttt) REVERT: U 54 MET cc_start: 0.8851 (mtm) cc_final: 0.8590 (mtm) REVERT: U 157 MET cc_start: 0.8881 (mpp) cc_final: 0.8467 (mpp) REVERT: U 326 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7535 (tm-30) REVERT: U 400 ASP cc_start: 0.8617 (t0) cc_final: 0.8377 (t0) REVERT: J 33 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8428 (mt-10) REVERT: J 71 GLU cc_start: 0.8497 (mp0) cc_final: 0.8061 (mp0) REVERT: J 82 SER cc_start: 0.9283 (p) cc_final: 0.9060 (p) REVERT: J 104 MET cc_start: 0.8432 (ttp) cc_final: 0.8014 (ttp) REVERT: V 184 GLN cc_start: 0.8324 (mp10) cc_final: 0.8031 (mp10) REVERT: V 261 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8252 (pt0) REVERT: V 323 LYS cc_start: 0.9486 (mmtt) cc_final: 0.9112 (mmmt) REVERT: K 15 LYS cc_start: 0.9029 (mtmm) cc_final: 0.7955 (mtmm) REVERT: K 33 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8380 (mt-10) REVERT: K 69 GLU cc_start: 0.7706 (pp20) cc_final: 0.6505 (pp20) REVERT: K 71 GLU cc_start: 0.8204 (mp0) cc_final: 0.7860 (mp0) REVERT: W 183 ASN cc_start: 0.9020 (t0) cc_final: 0.8691 (t0) REVERT: L 71 GLU cc_start: 0.8635 (mp0) cc_final: 0.8179 (mp0) REVERT: L 74 GLU cc_start: 0.8504 (tp30) cc_final: 0.8077 (tp30) REVERT: L 98 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8421 (mmtp) REVERT: X 157 MET cc_start: 0.8849 (mpp) cc_final: 0.8447 (mpp) REVERT: X 326 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7531 (tm-30) REVERT: X 357 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8089 (mmmm) REVERT: X 360 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7866 (mt-10) REVERT: X 400 ASP cc_start: 0.8631 (t0) cc_final: 0.8377 (t0) outliers start: 166 outliers final: 88 residues processed: 1221 average time/residue: 0.2435 time to fit residues: 487.6415 Evaluate side-chains 1157 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1062 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain M residue 375 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 375 ILE Chi-restraints excluded: chain O residue 395 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain P residue 261 GLU Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain P residue 375 ILE Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain Q residue 65 LYS Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain Q residue 375 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain R residue 65 LYS Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 375 ILE Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain S residue 275 VAL Chi-restraints excluded: chain S residue 375 ILE Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain T residue 65 LYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 375 ILE Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain U residue 375 ILE Chi-restraints excluded: chain U residue 395 GLU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 272 ILE Chi-restraints excluded: chain V residue 311 THR Chi-restraints excluded: chain V residue 375 ILE Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 375 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain X residue 375 ILE Chi-restraints excluded: chain X residue 395 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 156 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 402 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 340 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 381 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 516 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 158 GLN A 2 ASN N 299 ASN O 182 GLN D 2 ASN P 158 GLN P 299 ASN Q 158 GLN ** F 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 182 GLN S 158 GLN S 299 ASN T 158 GLN I 2 ASN U 182 GLN V 299 ASN W 158 GLN X 158 GLN ** X 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 299 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.058983 restraints weight = 119181.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.061350 restraints weight = 60051.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.062897 restraints weight = 39212.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.063910 restraints weight = 29833.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.064573 restraints weight = 25035.318| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 48816 Z= 0.288 Angle : 0.653 7.540 65844 Z= 0.348 Chirality : 0.043 0.133 7296 Planarity : 0.004 0.034 8544 Dihedral : 4.070 16.936 6588 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.18 % Favored : 93.00 % Rotamer: Outliers : 3.31 % Allowed : 22.15 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.11), residues: 6000 helix: 2.54 (0.10), residues: 3000 sheet: -1.28 (0.21), residues: 600 loop : -1.69 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 78 TYR 0.014 0.001 TYR U 265 PHE 0.013 0.002 PHE Q 338 TRP 0.010 0.002 TRP N 221 HIS 0.004 0.001 HIS I 58 Details of bonding type rmsd covalent geometry : bond 0.00666 (48816) covalent geometry : angle 0.65263 (65844) hydrogen bonds : bond 0.05896 ( 2400) hydrogen bonds : angle 4.63027 ( 7056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1035 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8636 (tp40) cc_final: 0.8372 (tp40) REVERT: B 11 GLU cc_start: 0.9128 (tp30) cc_final: 0.8651 (tp30) REVERT: B 33 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8406 (mt-10) REVERT: B 71 GLU cc_start: 0.8330 (mp0) cc_final: 0.7990 (mp0) REVERT: M 122 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8572 (mtm-85) REVERT: M 183 ASN cc_start: 0.9141 (t0) cc_final: 0.8778 (t0) REVERT: M 301 ASN cc_start: 0.8543 (t0) cc_final: 0.8224 (t0) REVERT: M 359 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8353 (pt0) REVERT: A 71 GLU cc_start: 0.8583 (mp0) cc_final: 0.8108 (mp0) REVERT: A 82 SER cc_start: 0.9355 (p) cc_final: 0.9127 (p) REVERT: N 145 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8559 (mp0) REVERT: N 183 ASN cc_start: 0.9083 (t0) cc_final: 0.8246 (t0) REVERT: N 184 GLN cc_start: 0.8428 (mp10) cc_final: 0.8016 (mp10) REVERT: N 261 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: N 362 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8764 (mt-10) REVERT: C 6 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8856 (mp) REVERT: C 71 GLU cc_start: 0.8562 (mp0) cc_final: 0.8005 (mp0) REVERT: C 74 GLU cc_start: 0.8490 (tp30) cc_final: 0.8065 (tp30) REVERT: C 98 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8404 (mmtp) REVERT: C 104 MET cc_start: 0.8726 (ttt) cc_final: 0.8460 (ttt) REVERT: O 54 MET cc_start: 0.8958 (mtm) cc_final: 0.8739 (mtm) REVERT: O 157 MET cc_start: 0.8933 (mpp) cc_final: 0.8549 (mpp) REVERT: O 197 ASP cc_start: 0.9061 (m-30) cc_final: 0.8847 (m-30) REVERT: O 326 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7599 (tm-30) REVERT: O 357 LYS cc_start: 0.8625 (mmmm) cc_final: 0.7876 (mmmm) REVERT: D 11 GLU cc_start: 0.9200 (tp30) cc_final: 0.8907 (tp30) REVERT: D 71 GLU cc_start: 0.8599 (mp0) cc_final: 0.8123 (mp0) REVERT: D 82 SER cc_start: 0.9360 (p) cc_final: 0.9127 (p) REVERT: P 68 LYS cc_start: 0.9345 (tppt) cc_final: 0.9003 (tppt) REVERT: P 145 GLU cc_start: 0.8586 (mp0) cc_final: 0.7949 (mp0) REVERT: P 183 ASN cc_start: 0.9094 (t0) cc_final: 0.8247 (t0) REVERT: P 184 GLN cc_start: 0.8430 (mp10) cc_final: 0.8016 (mp10) REVERT: P 261 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: P 359 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8569 (mt-10) REVERT: P 360 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8380 (mp0) REVERT: E 15 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8009 (mtmm) REVERT: E 33 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8404 (mt-10) REVERT: Q 183 ASN cc_start: 0.9147 (t0) cc_final: 0.8784 (t0) REVERT: Q 301 ASN cc_start: 0.8555 (t0) cc_final: 0.8229 (t0) REVERT: F 6 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8871 (mp) REVERT: F 71 GLU cc_start: 0.8585 (mp0) cc_final: 0.8080 (mp0) REVERT: F 74 GLU cc_start: 0.8794 (tp30) cc_final: 0.8240 (tp30) REVERT: F 78 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8250 (ptt90) REVERT: F 98 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8438 (mmtp) REVERT: F 104 MET cc_start: 0.8729 (ttt) cc_final: 0.8459 (ttt) REVERT: R 157 MET cc_start: 0.8958 (mpp) cc_final: 0.8627 (mpp) REVERT: R 197 ASP cc_start: 0.9055 (m-30) cc_final: 0.8846 (m-30) REVERT: G 11 GLU cc_start: 0.9173 (tp30) cc_final: 0.8837 (tp30) REVERT: G 33 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8435 (mt-10) REVERT: G 71 GLU cc_start: 0.8592 (mp0) cc_final: 0.8107 (mp0) REVERT: S 68 LYS cc_start: 0.9334 (tppt) cc_final: 0.9024 (tppt) REVERT: S 145 GLU cc_start: 0.8637 (mp0) cc_final: 0.8210 (mp0) REVERT: S 183 ASN cc_start: 0.9090 (t0) cc_final: 0.8322 (t0) REVERT: S 184 GLN cc_start: 0.8442 (mp10) cc_final: 0.8010 (mp10) REVERT: S 261 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: S 359 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8556 (mt-10) REVERT: S 360 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8437 (mp0) REVERT: H 15 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8077 (mtmm) REVERT: H 33 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8387 (mt-10) REVERT: H 71 GLU cc_start: 0.8232 (mp0) cc_final: 0.7898 (mp0) REVERT: T 79 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9068 (mp) REVERT: T 183 ASN cc_start: 0.9141 (t0) cc_final: 0.8778 (t0) REVERT: T 301 ASN cc_start: 0.8596 (t0) cc_final: 0.8285 (t0) REVERT: T 359 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8403 (pt0) REVERT: I 33 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8662 (mt-10) REVERT: I 71 GLU cc_start: 0.8702 (mp0) cc_final: 0.8221 (mp0) REVERT: I 74 GLU cc_start: 0.8615 (tp30) cc_final: 0.8168 (tp30) REVERT: I 98 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8416 (mmtp) REVERT: I 104 MET cc_start: 0.8726 (ttt) cc_final: 0.8442 (ttt) REVERT: U 54 MET cc_start: 0.8964 (mtm) cc_final: 0.8752 (mtm) REVERT: U 145 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8956 (mp0) REVERT: U 157 MET cc_start: 0.8961 (mpp) cc_final: 0.8548 (mpp) REVERT: U 197 ASP cc_start: 0.9055 (m-30) cc_final: 0.8841 (m-30) REVERT: U 327 ASP cc_start: 0.8616 (m-30) cc_final: 0.8345 (m-30) REVERT: J 11 GLU cc_start: 0.9195 (tp30) cc_final: 0.8855 (tp30) REVERT: J 71 GLU cc_start: 0.8564 (mp0) cc_final: 0.8066 (mp0) REVERT: J 82 SER cc_start: 0.9364 (p) cc_final: 0.9126 (p) REVERT: V 104 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7051 (t70) REVERT: V 145 GLU cc_start: 0.8861 (mp0) cc_final: 0.8227 (mp0) REVERT: V 183 ASN cc_start: 0.9100 (t0) cc_final: 0.8336 (t0) REVERT: V 184 GLN cc_start: 0.8448 (mp10) cc_final: 0.8015 (mp10) REVERT: V 261 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: V 323 LYS cc_start: 0.9509 (mmtt) cc_final: 0.9109 (mmmt) REVERT: K 15 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8024 (mtmm) REVERT: K 33 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8424 (mt-10) REVERT: K 71 GLU cc_start: 0.8275 (mp0) cc_final: 0.7835 (mp0) REVERT: W 183 ASN cc_start: 0.9138 (t0) cc_final: 0.8778 (t0) REVERT: W 301 ASN cc_start: 0.8618 (t0) cc_final: 0.8306 (t0) REVERT: W 359 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8416 (pt0) REVERT: L 6 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8872 (mp) REVERT: L 33 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8657 (mt-10) REVERT: L 45 LYS cc_start: 0.9500 (mttp) cc_final: 0.9129 (mttm) REVERT: L 71 GLU cc_start: 0.8690 (mp0) cc_final: 0.8237 (mp0) REVERT: L 98 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8406 (mmtp) REVERT: L 104 MET cc_start: 0.8746 (ttt) cc_final: 0.8403 (ttt) REVERT: X 65 LYS cc_start: 0.9087 (pttp) cc_final: 0.8808 (pttp) REVERT: X 145 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8964 (mp0) REVERT: X 157 MET cc_start: 0.8928 (mpp) cc_final: 0.8567 (mpp) REVERT: X 197 ASP cc_start: 0.9071 (m-30) cc_final: 0.8858 (m-30) REVERT: X 299 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.9011 (t0) REVERT: X 357 LYS cc_start: 0.8637 (mmmm) cc_final: 0.7863 (mmmm) outliers start: 172 outliers final: 114 residues processed: 1178 average time/residue: 0.2832 time to fit residues: 548.9576 Evaluate side-chains 1128 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1003 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain N residue 264 GLU Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 376 THR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 272 ILE Chi-restraints excluded: chain O residue 315 THR Chi-restraints excluded: chain O residue 376 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain P residue 178 GLN Chi-restraints excluded: chain P residue 229 MET Chi-restraints excluded: chain P residue 261 GLU Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain Q residue 78 LYS Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 264 GLU Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 272 ILE Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain U residue 272 ILE Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain U residue 315 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain V residue 101 ILE Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 178 GLN Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 264 GLU Chi-restraints excluded: chain V residue 272 ILE Chi-restraints excluded: chain V residue 311 THR Chi-restraints excluded: chain V residue 376 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 294 GLU Chi-restraints excluded: chain X residue 299 ASN Chi-restraints excluded: chain X residue 315 THR Chi-restraints excluded: chain X residue 395 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 535 optimal weight: 10.0000 chunk 413 optimal weight: 3.9990 chunk 151 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 528 optimal weight: 2.9990 chunk 329 optimal weight: 0.9990 chunk 437 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 420 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 182 GLN R 182 GLN U 182 GLN ** X 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.085634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.062656 restraints weight = 117097.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.065130 restraints weight = 58396.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.066763 restraints weight = 37847.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.067840 restraints weight = 28577.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.068496 restraints weight = 23841.355| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 48816 Z= 0.124 Angle : 0.567 8.007 65844 Z= 0.302 Chirality : 0.040 0.144 7296 Planarity : 0.003 0.035 8544 Dihedral : 3.826 18.447 6588 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.80 % Allowed : 4.57 % Favored : 94.63 % Rotamer: Outliers : 2.62 % Allowed : 23.71 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.11), residues: 6000 helix: 3.00 (0.10), residues: 2868 sheet: -0.99 (0.21), residues: 588 loop : -1.42 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 78 TYR 0.008 0.001 TYR M 37 PHE 0.011 0.001 PHE L 83 TRP 0.006 0.001 TRP O 89 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00281 (48816) covalent geometry : angle 0.56659 (65844) hydrogen bonds : bond 0.03837 ( 2400) hydrogen bonds : angle 4.15959 ( 7056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1100 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 GLU cc_start: 0.9116 (tp30) cc_final: 0.8538 (tp30) REVERT: B 33 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8436 (mt-10) REVERT: B 71 GLU cc_start: 0.8283 (mp0) cc_final: 0.7821 (mp0) REVERT: M 183 ASN cc_start: 0.9113 (t0) cc_final: 0.8727 (t0) REVERT: M 301 ASN cc_start: 0.8244 (t0) cc_final: 0.7851 (t0) REVERT: M 398 LEU cc_start: 0.8859 (tp) cc_final: 0.8657 (tp) REVERT: A 15 LYS cc_start: 0.9464 (ttmm) cc_final: 0.8936 (mtmm) REVERT: A 33 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 71 GLU cc_start: 0.8564 (mp0) cc_final: 0.8099 (mp0) REVERT: A 82 SER cc_start: 0.9231 (p) cc_final: 0.9021 (p) REVERT: A 104 MET cc_start: 0.8778 (ttp) cc_final: 0.8521 (ttp) REVERT: N 157 MET cc_start: 0.8908 (mpp) cc_final: 0.8397 (mpp) REVERT: N 183 ASN cc_start: 0.9109 (t0) cc_final: 0.8532 (t0) REVERT: N 184 GLN cc_start: 0.8507 (mp10) cc_final: 0.8054 (mp10) REVERT: N 261 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: N 362 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8716 (mt-10) REVERT: C 6 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8917 (mp) REVERT: C 71 GLU cc_start: 0.8528 (mp0) cc_final: 0.7949 (mp0) REVERT: C 98 LYS cc_start: 0.8671 (mmtp) cc_final: 0.8449 (mmtp) REVERT: C 104 MET cc_start: 0.8561 (ttt) cc_final: 0.8337 (ttt) REVERT: O 52 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8709 (mt-10) REVERT: O 54 MET cc_start: 0.8906 (mtm) cc_final: 0.8669 (mtm) REVERT: O 68 LYS cc_start: 0.9332 (tppt) cc_final: 0.8989 (tppt) REVERT: O 145 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8919 (mp0) REVERT: O 157 MET cc_start: 0.8909 (mpp) cc_final: 0.8539 (mpp) REVERT: O 326 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7523 (tm-30) REVERT: D 11 GLU cc_start: 0.9112 (tp30) cc_final: 0.8863 (tp30) REVERT: D 33 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8508 (mt-10) REVERT: D 71 GLU cc_start: 0.8582 (mp0) cc_final: 0.8075 (mp0) REVERT: D 82 SER cc_start: 0.9254 (p) cc_final: 0.9023 (p) REVERT: P 68 LYS cc_start: 0.9318 (tppt) cc_final: 0.9043 (tppt) REVERT: P 145 GLU cc_start: 0.8531 (mp0) cc_final: 0.7822 (mp0) REVERT: P 157 MET cc_start: 0.8790 (mpp) cc_final: 0.8466 (mpp) REVERT: P 183 ASN cc_start: 0.9111 (t0) cc_final: 0.8498 (t0) REVERT: P 184 GLN cc_start: 0.8510 (mp10) cc_final: 0.8051 (mp10) REVERT: P 261 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: P 359 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8560 (mt-10) REVERT: P 362 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8935 (mt-10) REVERT: E 11 GLU cc_start: 0.9120 (tp30) cc_final: 0.8763 (tp30) REVERT: E 15 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8908 (ttmm) REVERT: E 33 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8471 (mt-10) REVERT: E 67 LYS cc_start: 0.9053 (mmtm) cc_final: 0.8831 (mmtm) REVERT: E 71 GLU cc_start: 0.8371 (mp0) cc_final: 0.7815 (mp0) REVERT: Q 132 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8492 (mm-30) REVERT: Q 183 ASN cc_start: 0.9115 (t0) cc_final: 0.8726 (t0) REVERT: Q 301 ASN cc_start: 0.8235 (t0) cc_final: 0.7844 (t0) REVERT: Q 359 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8347 (pt0) REVERT: F 6 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8918 (mp) REVERT: F 71 GLU cc_start: 0.8559 (mp0) cc_final: 0.8047 (mp0) REVERT: F 74 GLU cc_start: 0.8738 (tp30) cc_final: 0.8332 (tp30) REVERT: F 104 MET cc_start: 0.8670 (ttt) cc_final: 0.8451 (ttt) REVERT: R 145 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8893 (mp0) REVERT: R 157 MET cc_start: 0.8924 (mpp) cc_final: 0.8487 (mpp) REVERT: R 183 ASN cc_start: 0.9106 (t0) cc_final: 0.8373 (t0) REVERT: G 33 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8493 (mt-10) REVERT: G 71 GLU cc_start: 0.8560 (mp0) cc_final: 0.8041 (mp0) REVERT: S 68 LYS cc_start: 0.9271 (tppt) cc_final: 0.8968 (tppt) REVERT: S 145 GLU cc_start: 0.8581 (mp0) cc_final: 0.8118 (mp0) REVERT: S 157 MET cc_start: 0.8815 (mpp) cc_final: 0.8486 (mpp) REVERT: S 183 ASN cc_start: 0.9065 (t0) cc_final: 0.8468 (t0) REVERT: S 184 GLN cc_start: 0.8517 (mp10) cc_final: 0.8065 (mp10) REVERT: S 261 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: S 321 ASP cc_start: 0.8940 (t0) cc_final: 0.8611 (t0) REVERT: S 359 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8483 (mt-10) REVERT: S 362 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8476 (mt-10) REVERT: S 398 LEU cc_start: 0.8924 (tp) cc_final: 0.8705 (tp) REVERT: H 11 GLU cc_start: 0.9114 (tp30) cc_final: 0.8754 (tp30) REVERT: H 15 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8900 (ttmm) REVERT: H 33 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8483 (mt-10) REVERT: H 71 GLU cc_start: 0.8082 (mp0) cc_final: 0.7742 (mp0) REVERT: H 72 ASP cc_start: 0.8689 (p0) cc_final: 0.8455 (p0) REVERT: H 75 SER cc_start: 0.9457 (p) cc_final: 0.9175 (p) REVERT: T 79 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9051 (mp) REVERT: T 180 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7469 (ttm-80) REVERT: T 183 ASN cc_start: 0.9114 (t0) cc_final: 0.8703 (t0) REVERT: T 301 ASN cc_start: 0.8294 (t0) cc_final: 0.7912 (t0) REVERT: I 33 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8565 (mt-10) REVERT: I 71 GLU cc_start: 0.8689 (mp0) cc_final: 0.8188 (mp0) REVERT: I 74 GLU cc_start: 0.8584 (tp30) cc_final: 0.8263 (tp30) REVERT: I 98 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8468 (mmtp) REVERT: U 54 MET cc_start: 0.8913 (mtm) cc_final: 0.8662 (mtm) REVERT: U 68 LYS cc_start: 0.9346 (tppt) cc_final: 0.8934 (tppt) REVERT: U 145 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8949 (mp0) REVERT: U 157 MET cc_start: 0.8919 (mpp) cc_final: 0.8462 (mpp) REVERT: J 3 GLN cc_start: 0.8680 (tp40) cc_final: 0.8376 (tp40) REVERT: J 33 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8462 (mt-10) REVERT: J 71 GLU cc_start: 0.8594 (mp0) cc_final: 0.8112 (mp0) REVERT: J 82 SER cc_start: 0.9263 (p) cc_final: 0.9032 (p) REVERT: V 104 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6963 (t70) REVERT: V 145 GLU cc_start: 0.8777 (mp0) cc_final: 0.8409 (mp0) REVERT: V 157 MET cc_start: 0.8891 (mpp) cc_final: 0.8350 (mpp) REVERT: V 183 ASN cc_start: 0.9069 (t0) cc_final: 0.8474 (t0) REVERT: V 184 GLN cc_start: 0.8516 (mp10) cc_final: 0.8066 (mp10) REVERT: V 261 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: V 323 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9189 (mmmt) REVERT: K 11 GLU cc_start: 0.9107 (tp30) cc_final: 0.8751 (tp30) REVERT: K 15 LYS cc_start: 0.9104 (mtmm) cc_final: 0.8892 (ttmm) REVERT: K 33 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8461 (mt-10) REVERT: K 71 GLU cc_start: 0.8135 (mp0) cc_final: 0.7689 (mp0) REVERT: W 180 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7428 (ttm-80) REVERT: W 183 ASN cc_start: 0.9112 (t0) cc_final: 0.8700 (t0) REVERT: W 301 ASN cc_start: 0.8253 (t0) cc_final: 0.7847 (t0) REVERT: W 398 LEU cc_start: 0.8840 (tp) cc_final: 0.8637 (tp) REVERT: L 6 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8923 (mp) REVERT: L 33 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8584 (mt-10) REVERT: L 45 LYS cc_start: 0.9483 (mttp) cc_final: 0.9119 (mttm) REVERT: L 71 GLU cc_start: 0.8665 (mp0) cc_final: 0.8191 (mp0) REVERT: L 98 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8450 (mmtp) REVERT: L 104 MET cc_start: 0.8640 (ttt) cc_final: 0.8411 (ttt) REVERT: X 68 LYS cc_start: 0.9310 (tppt) cc_final: 0.9047 (tppt) REVERT: X 145 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8943 (mp0) REVERT: X 157 MET cc_start: 0.8911 (mpp) cc_final: 0.8561 (mpp) REVERT: X 357 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8743 (mmmm) outliers start: 136 outliers final: 79 residues processed: 1194 average time/residue: 0.2277 time to fit residues: 443.6022 Evaluate side-chains 1138 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1048 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 357 LYS Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain P residue 261 GLU Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 180 ARG Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 178 GLN Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 272 ILE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 180 ARG Chi-restraints excluded: chain W residue 294 GLU Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 294 GLU Chi-restraints excluded: chain X residue 395 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 561 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 391 optimal weight: 3.9990 chunk 429 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 434 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 369 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 218 GLN U 218 GLN ** X 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 218 GLN X 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.084118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.061109 restraints weight = 117698.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.063536 restraints weight = 58844.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.065141 restraints weight = 38276.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.066205 restraints weight = 28991.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.066819 restraints weight = 24244.513| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 48816 Z= 0.173 Angle : 0.595 8.723 65844 Z= 0.316 Chirality : 0.040 0.146 7296 Planarity : 0.003 0.034 8544 Dihedral : 3.850 19.136 6588 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.80 % Allowed : 5.35 % Favored : 93.85 % Rotamer: Outliers : 2.39 % Allowed : 24.46 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.11), residues: 6000 helix: 2.96 (0.10), residues: 2856 sheet: -1.20 (0.22), residues: 552 loop : -1.26 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 78 TYR 0.009 0.001 TYR X 265 PHE 0.010 0.001 PHE M 338 TRP 0.006 0.001 TRP Q 89 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd covalent geometry : bond 0.00404 (48816) covalent geometry : angle 0.59481 (65844) hydrogen bonds : bond 0.04476 ( 2400) hydrogen bonds : angle 4.23948 ( 7056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1042 time to evaluate : 1.165 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: B 11 GLU cc_start: 0.9110 (tp30) cc_final: 0.8548 (tp30) REVERT: B 33 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8453 (mt-10) REVERT: B 71 GLU cc_start: 0.8426 (mp0) cc_final: 0.8001 (mp0) REVERT: M 183 ASN cc_start: 0.9149 (t0) cc_final: 0.8772 (t0) REVERT: M 301 ASN cc_start: 0.8547 (t0) cc_final: 0.8335 (t0) REVERT: M 359 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8410 (pt0) REVERT: M 398 LEU cc_start: 0.8941 (tp) cc_final: 0.8716 (tp) REVERT: A 11 GLU cc_start: 0.9140 (tp30) cc_final: 0.8629 (tp30) REVERT: A 15 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9107 (ttmm) REVERT: A 71 GLU cc_start: 0.8569 (mp0) cc_final: 0.8097 (mp0) REVERT: A 82 SER cc_start: 0.9247 (p) cc_final: 0.9029 (p) REVERT: A 88 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8578 (mm-30) REVERT: N 145 GLU cc_start: 0.8873 (mp0) cc_final: 0.8276 (mp0) REVERT: N 157 MET cc_start: 0.9060 (mpp) cc_final: 0.8494 (mpp) REVERT: N 183 ASN cc_start: 0.9113 (t0) cc_final: 0.8515 (t0) REVERT: N 184 GLN cc_start: 0.8517 (mp10) cc_final: 0.8062 (mp10) REVERT: N 261 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: N 362 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8682 (mt-10) REVERT: N 398 LEU cc_start: 0.8627 (tp) cc_final: 0.8409 (tp) REVERT: C 6 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8825 (mp) REVERT: C 71 GLU cc_start: 0.8529 (mp0) cc_final: 0.7992 (mp0) REVERT: C 104 MET cc_start: 0.8597 (ttt) cc_final: 0.8391 (ttt) REVERT: O 52 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8714 (mt-10) REVERT: O 54 MET cc_start: 0.8923 (mtm) cc_final: 0.8681 (mtm) REVERT: O 145 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8896 (mp0) REVERT: O 157 MET cc_start: 0.8931 (mpp) cc_final: 0.8554 (mpp) REVERT: O 183 ASN cc_start: 0.9139 (t0) cc_final: 0.8384 (t0) REVERT: D 11 GLU cc_start: 0.9167 (tp30) cc_final: 0.8929 (tp30) REVERT: D 33 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8412 (mt-10) REVERT: D 71 GLU cc_start: 0.8552 (mp0) cc_final: 0.8064 (mp0) REVERT: D 82 SER cc_start: 0.9260 (p) cc_final: 0.9032 (p) REVERT: D 88 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8578 (mm-30) REVERT: P 68 LYS cc_start: 0.9319 (tppt) cc_final: 0.9017 (tppt) REVERT: P 145 GLU cc_start: 0.8550 (mp0) cc_final: 0.8060 (mp0) REVERT: P 157 MET cc_start: 0.8836 (mpp) cc_final: 0.8500 (mpp) REVERT: P 183 ASN cc_start: 0.9107 (t0) cc_final: 0.8501 (t0) REVERT: P 184 GLN cc_start: 0.8520 (mp10) cc_final: 0.8062 (mp10) REVERT: P 247 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8310 (p0) REVERT: P 261 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: P 359 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8551 (mt-10) REVERT: P 362 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8915 (mt-10) REVERT: E 11 GLU cc_start: 0.9123 (tp30) cc_final: 0.8707 (tp30) REVERT: E 15 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8857 (ttmm) REVERT: E 33 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8433 (mt-10) REVERT: E 71 GLU cc_start: 0.8079 (mp0) cc_final: 0.7811 (mp0) REVERT: Q 132 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8497 (mm-30) REVERT: Q 183 ASN cc_start: 0.9147 (t0) cc_final: 0.8769 (t0) REVERT: Q 301 ASN cc_start: 0.8545 (t0) cc_final: 0.8331 (t0) REVERT: Q 398 LEU cc_start: 0.8638 (tp) cc_final: 0.8419 (tp) REVERT: F 6 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8882 (mp) REVERT: F 71 GLU cc_start: 0.8543 (mp0) cc_final: 0.7997 (mp0) REVERT: F 78 ARG cc_start: 0.9001 (ptt90) cc_final: 0.7856 (ptt90) REVERT: F 104 MET cc_start: 0.8635 (ttt) cc_final: 0.8428 (ttt) REVERT: F 120 ARG cc_start: 0.8838 (tpt-90) cc_final: 0.8433 (ttt-90) REVERT: R 145 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8883 (mp0) REVERT: R 157 MET cc_start: 0.8944 (mpp) cc_final: 0.8496 (mpp) REVERT: R 183 ASN cc_start: 0.9149 (t0) cc_final: 0.8398 (t0) REVERT: R 326 GLU cc_start: 0.7753 (tm-30) cc_final: 0.6928 (tm-30) REVERT: R 400 ASP cc_start: 0.8620 (t0) cc_final: 0.8390 (t0) REVERT: G 11 GLU cc_start: 0.9124 (tp30) cc_final: 0.8787 (tp30) REVERT: G 71 GLU cc_start: 0.8544 (mp0) cc_final: 0.8012 (mp0) REVERT: S 68 LYS cc_start: 0.9298 (tppt) cc_final: 0.8982 (tppt) REVERT: S 145 GLU cc_start: 0.8634 (mp0) cc_final: 0.8040 (mp0) REVERT: S 157 MET cc_start: 0.8866 (mpp) cc_final: 0.8513 (mpp) REVERT: S 183 ASN cc_start: 0.9117 (t0) cc_final: 0.8511 (t0) REVERT: S 184 GLN cc_start: 0.8531 (mp10) cc_final: 0.8079 (mp10) REVERT: S 261 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: S 359 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8528 (mt-10) REVERT: H 11 GLU cc_start: 0.9120 (tp30) cc_final: 0.8703 (tp30) REVERT: H 15 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8870 (ttmm) REVERT: H 33 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8269 (mp0) REVERT: H 71 GLU cc_start: 0.8117 (mp0) cc_final: 0.7723 (mp0) REVERT: T 79 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9084 (mp) REVERT: T 183 ASN cc_start: 0.9151 (t0) cc_final: 0.8770 (t0) REVERT: T 359 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8397 (pt0) REVERT: T 398 LEU cc_start: 0.8679 (tp) cc_final: 0.8458 (tp) REVERT: I 11 GLU cc_start: 0.9235 (tp30) cc_final: 0.8847 (tp30) REVERT: I 33 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8587 (mt-10) REVERT: I 71 GLU cc_start: 0.8652 (mp0) cc_final: 0.8102 (mp0) REVERT: I 74 GLU cc_start: 0.8620 (tp30) cc_final: 0.8286 (tp30) REVERT: I 104 MET cc_start: 0.8538 (ttt) cc_final: 0.8326 (ttt) REVERT: U 52 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8709 (mt-10) REVERT: U 54 MET cc_start: 0.8936 (mtm) cc_final: 0.8699 (mtm) REVERT: U 157 MET cc_start: 0.8943 (mpp) cc_final: 0.8467 (mpp) REVERT: U 183 ASN cc_start: 0.9135 (t0) cc_final: 0.8353 (t0) REVERT: U 326 GLU cc_start: 0.7792 (tm-30) cc_final: 0.6982 (tm-30) REVERT: J 11 GLU cc_start: 0.9153 (tp30) cc_final: 0.8786 (tp30) REVERT: J 33 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8485 (mt-10) REVERT: J 82 SER cc_start: 0.9254 (p) cc_final: 0.9032 (p) REVERT: J 88 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8568 (mm-30) REVERT: V 104 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6998 (t70) REVERT: V 145 GLU cc_start: 0.8834 (mp0) cc_final: 0.8449 (mp0) REVERT: V 157 MET cc_start: 0.8934 (mpp) cc_final: 0.8353 (mpp) REVERT: V 183 ASN cc_start: 0.9119 (t0) cc_final: 0.8515 (t0) REVERT: V 184 GLN cc_start: 0.8531 (mp10) cc_final: 0.8079 (mp10) REVERT: V 261 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: V 323 LYS cc_start: 0.9477 (mmtt) cc_final: 0.9106 (mmmt) REVERT: K 11 GLU cc_start: 0.9114 (tp30) cc_final: 0.8691 (tp30) REVERT: K 15 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8864 (ttmm) REVERT: K 33 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8254 (mp0) REVERT: K 71 GLU cc_start: 0.8241 (mp0) cc_final: 0.7818 (mp0) REVERT: W 183 ASN cc_start: 0.9149 (t0) cc_final: 0.8766 (t0) REVERT: W 301 ASN cc_start: 0.8612 (t0) cc_final: 0.8403 (t0) REVERT: W 359 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8396 (pt0) REVERT: W 398 LEU cc_start: 0.8883 (tp) cc_final: 0.8654 (tp) REVERT: L 6 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8897 (mp) REVERT: L 45 LYS cc_start: 0.9504 (mttp) cc_final: 0.9150 (mttm) REVERT: L 71 GLU cc_start: 0.8635 (mp0) cc_final: 0.8143 (mp0) REVERT: L 104 MET cc_start: 0.8533 (ttt) cc_final: 0.8317 (ttt) REVERT: X 157 MET cc_start: 0.8936 (mpp) cc_final: 0.8579 (mpp) REVERT: X 326 GLU cc_start: 0.7772 (tm-30) cc_final: 0.6962 (tm-30) outliers start: 124 outliers final: 102 residues processed: 1135 average time/residue: 0.1923 time to fit residues: 358.6958 Evaluate side-chains 1122 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1010 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain M residue 258 ILE Chi-restraints excluded: chain M residue 272 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 357 LYS Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 272 ILE Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 315 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain P residue 178 GLN Chi-restraints excluded: chain P residue 247 ASP Chi-restraints excluded: chain P residue 261 GLU Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain Q residue 65 LYS Chi-restraints excluded: chain Q residue 78 LYS Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain T residue 65 LYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 272 ILE Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain U residue 272 ILE Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 178 GLN Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 272 ILE Chi-restraints excluded: chain V residue 311 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain W residue 65 LYS Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 294 GLU Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 272 ILE Chi-restraints excluded: chain X residue 294 GLU Chi-restraints excluded: chain X residue 395 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 499 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 471 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 430 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 498 optimal weight: 0.9990 chunk 299 optimal weight: 0.0470 chunk 462 optimal weight: 6.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 218 GLN V 402 ASN ** X 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.084881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.061918 restraints weight = 117096.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.064363 restraints weight = 58550.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.065969 restraints weight = 38030.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.067044 restraints weight = 28813.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.067728 restraints weight = 24092.534| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48816 Z= 0.147 Angle : 0.593 9.446 65844 Z= 0.314 Chirality : 0.040 0.151 7296 Planarity : 0.003 0.040 8544 Dihedral : 3.799 18.156 6588 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.80 % Allowed : 4.78 % Favored : 94.42 % Rotamer: Outliers : 2.35 % Allowed : 24.63 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.11), residues: 6000 helix: 2.92 (0.10), residues: 2880 sheet: -0.91 (0.23), residues: 528 loop : -1.24 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 78 TYR 0.007 0.001 TYR R 265 PHE 0.012 0.001 PHE T 338 TRP 0.007 0.001 TRP O 89 HIS 0.004 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00344 (48816) covalent geometry : angle 0.59335 (65844) hydrogen bonds : bond 0.04093 ( 2400) hydrogen bonds : angle 4.14973 ( 7056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1046 time to evaluate : 1.165 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: B 11 GLU cc_start: 0.9098 (tp30) cc_final: 0.8516 (tp30) REVERT: B 33 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8215 (mp0) REVERT: B 71 GLU cc_start: 0.8450 (mp0) cc_final: 0.8010 (mp0) REVERT: M 183 ASN cc_start: 0.9149 (t0) cc_final: 0.8772 (t0) REVERT: M 301 ASN cc_start: 0.8498 (t0) cc_final: 0.8290 (t0) REVERT: M 359 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8397 (pt0) REVERT: M 398 LEU cc_start: 0.9032 (tp) cc_final: 0.8810 (tp) REVERT: A 82 SER cc_start: 0.9227 (p) cc_final: 0.8998 (p) REVERT: N 145 GLU cc_start: 0.8845 (mp0) cc_final: 0.8249 (mp0) REVERT: N 157 MET cc_start: 0.9027 (mpp) cc_final: 0.8468 (mpp) REVERT: N 183 ASN cc_start: 0.9128 (t0) cc_final: 0.8599 (t0) REVERT: N 184 GLN cc_start: 0.8528 (mp10) cc_final: 0.8078 (mp10) REVERT: N 261 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8202 (pt0) REVERT: N 362 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8673 (mt-10) REVERT: N 398 LEU cc_start: 0.8652 (tp) cc_final: 0.8418 (tp) REVERT: C 6 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8876 (mp) REVERT: C 70 ASP cc_start: 0.8385 (p0) cc_final: 0.8146 (p0) REVERT: C 71 GLU cc_start: 0.8532 (mp0) cc_final: 0.7975 (mp0) REVERT: O 52 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8711 (mt-10) REVERT: O 54 MET cc_start: 0.8903 (mtm) cc_final: 0.8660 (mtm) REVERT: O 145 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8929 (mp0) REVERT: O 157 MET cc_start: 0.8924 (mpp) cc_final: 0.8525 (mpp) REVERT: O 183 ASN cc_start: 0.9143 (t0) cc_final: 0.8360 (t0) REVERT: O 362 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8705 (mt-10) REVERT: D 11 GLU cc_start: 0.9142 (tp30) cc_final: 0.8895 (tp30) REVERT: D 71 GLU cc_start: 0.8543 (mp0) cc_final: 0.8046 (mp0) REVERT: D 82 SER cc_start: 0.9236 (p) cc_final: 0.9003 (p) REVERT: P 68 LYS cc_start: 0.9266 (tppt) cc_final: 0.8966 (tppt) REVERT: P 145 GLU cc_start: 0.8536 (mp0) cc_final: 0.8034 (mp0) REVERT: P 157 MET cc_start: 0.8817 (mpp) cc_final: 0.8463 (mpp) REVERT: P 183 ASN cc_start: 0.9127 (t0) cc_final: 0.8594 (t0) REVERT: P 184 GLN cc_start: 0.8529 (mp10) cc_final: 0.8076 (mp10) REVERT: P 261 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8308 (pt0) REVERT: P 359 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8469 (mt-10) REVERT: P 362 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8931 (mt-10) REVERT: E 11 GLU cc_start: 0.9106 (tp30) cc_final: 0.8693 (tp30) REVERT: E 15 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8860 (ttmm) REVERT: E 71 GLU cc_start: 0.8336 (mp0) cc_final: 0.7785 (mp0) REVERT: Q 183 ASN cc_start: 0.9153 (t0) cc_final: 0.8770 (t0) REVERT: Q 301 ASN cc_start: 0.8497 (t0) cc_final: 0.8290 (t0) REVERT: Q 359 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8389 (pt0) REVERT: Q 398 LEU cc_start: 0.8646 (tp) cc_final: 0.8399 (tp) REVERT: F 6 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8934 (mp) REVERT: F 70 ASP cc_start: 0.8412 (p0) cc_final: 0.8132 (p0) REVERT: F 71 GLU cc_start: 0.8557 (mp0) cc_final: 0.8001 (mp0) REVERT: F 74 GLU cc_start: 0.8290 (tp30) cc_final: 0.7752 (tp30) REVERT: F 78 ARG cc_start: 0.8846 (ptt90) cc_final: 0.8591 (ptt90) REVERT: F 120 ARG cc_start: 0.8800 (tpt-90) cc_final: 0.8325 (ttt-90) REVERT: R 68 LYS cc_start: 0.9316 (tppt) cc_final: 0.9014 (tppt) REVERT: R 145 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8899 (mp0) REVERT: R 157 MET cc_start: 0.8933 (mpp) cc_final: 0.8480 (mpp) REVERT: R 183 ASN cc_start: 0.9152 (t0) cc_final: 0.8369 (t0) REVERT: R 326 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7196 (tm-30) REVERT: R 359 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8576 (pt0) REVERT: G 11 GLU cc_start: 0.9124 (tp30) cc_final: 0.8916 (tp30) REVERT: G 71 GLU cc_start: 0.8539 (mp0) cc_final: 0.8020 (mp0) REVERT: S 68 LYS cc_start: 0.9260 (tppt) cc_final: 0.8934 (tppt) REVERT: S 145 GLU cc_start: 0.8619 (mp0) cc_final: 0.8157 (mp0) REVERT: S 157 MET cc_start: 0.8852 (mpp) cc_final: 0.8488 (mpp) REVERT: S 183 ASN cc_start: 0.9126 (t0) cc_final: 0.8508 (t0) REVERT: S 184 GLN cc_start: 0.8535 (mp10) cc_final: 0.8079 (mp10) REVERT: S 261 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: S 321 ASP cc_start: 0.8941 (t0) cc_final: 0.8616 (t0) REVERT: S 359 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8400 (mt-10) REVERT: S 398 LEU cc_start: 0.8943 (tp) cc_final: 0.8736 (tp) REVERT: H 11 GLU cc_start: 0.9107 (tp30) cc_final: 0.8671 (tp30) REVERT: H 15 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8850 (ttmm) REVERT: H 33 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8251 (mp0) REVERT: H 71 GLU cc_start: 0.8110 (mp0) cc_final: 0.7897 (mp0) REVERT: H 72 ASP cc_start: 0.8670 (p0) cc_final: 0.8433 (p0) REVERT: H 75 SER cc_start: 0.9464 (p) cc_final: 0.9216 (p) REVERT: T 79 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9070 (mp) REVERT: T 183 ASN cc_start: 0.9153 (t0) cc_final: 0.8771 (t0) REVERT: T 301 ASN cc_start: 0.8668 (t0) cc_final: 0.8385 (t0) REVERT: T 359 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8380 (pt0) REVERT: T 398 LEU cc_start: 0.8655 (tp) cc_final: 0.8402 (tp) REVERT: I 11 GLU cc_start: 0.9250 (tp30) cc_final: 0.8820 (tp30) REVERT: I 33 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8546 (mt-10) REVERT: I 71 GLU cc_start: 0.8611 (mp0) cc_final: 0.8062 (mp0) REVERT: I 74 GLU cc_start: 0.8598 (tp30) cc_final: 0.8260 (tp30) REVERT: U 52 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8698 (mt-10) REVERT: U 54 MET cc_start: 0.8903 (mtm) cc_final: 0.8665 (mtm) REVERT: U 68 LYS cc_start: 0.9303 (tppt) cc_final: 0.9036 (tppt) REVERT: U 145 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8883 (mp0) REVERT: U 157 MET cc_start: 0.8935 (mpp) cc_final: 0.8453 (mpp) REVERT: U 183 ASN cc_start: 0.9139 (t0) cc_final: 0.8359 (t0) REVERT: U 326 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7269 (tm-30) REVERT: U 359 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8556 (pt0) REVERT: J 11 GLU cc_start: 0.9119 (tp30) cc_final: 0.8852 (tp30) REVERT: J 71 GLU cc_start: 0.8325 (mp0) cc_final: 0.7892 (mp0) REVERT: J 82 SER cc_start: 0.9248 (p) cc_final: 0.9020 (p) REVERT: V 145 GLU cc_start: 0.8804 (mp0) cc_final: 0.8420 (mp0) REVERT: V 157 MET cc_start: 0.8933 (mpp) cc_final: 0.8329 (mpp) REVERT: V 183 ASN cc_start: 0.9128 (t0) cc_final: 0.8514 (t0) REVERT: V 184 GLN cc_start: 0.8542 (mp10) cc_final: 0.8085 (mp10) REVERT: V 261 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: V 323 LYS cc_start: 0.9508 (mmtt) cc_final: 0.9132 (mmmt) REVERT: V 362 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8423 (mt-10) REVERT: K 11 GLU cc_start: 0.9097 (tp30) cc_final: 0.8684 (tp30) REVERT: K 15 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8873 (ttmm) REVERT: K 71 GLU cc_start: 0.8082 (mp0) cc_final: 0.7697 (mp0) REVERT: W 183 ASN cc_start: 0.9146 (t0) cc_final: 0.8761 (t0) REVERT: W 359 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8377 (pt0) REVERT: L 6 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8900 (mp) REVERT: L 45 LYS cc_start: 0.9451 (mttp) cc_final: 0.9104 (mttm) REVERT: L 71 GLU cc_start: 0.8660 (mp0) cc_final: 0.8154 (mp0) REVERT: L 78 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7864 (ptt90) REVERT: X 145 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8874 (mp0) REVERT: X 157 MET cc_start: 0.8942 (mpp) cc_final: 0.8569 (mpp) REVERT: X 326 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7234 (tm-30) REVERT: X 359 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8544 (pt0) outliers start: 122 outliers final: 95 residues processed: 1133 average time/residue: 0.1876 time to fit residues: 348.6885 Evaluate side-chains 1130 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1027 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain M residue 272 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 395 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain P residue 178 GLN Chi-restraints excluded: chain P residue 261 GLU Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain Q residue 65 LYS Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain Q residue 395 GLU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 107 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain T residue 65 LYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 272 ILE Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain T residue 391 SER Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 178 GLN Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 272 ILE Chi-restraints excluded: chain V residue 275 VAL Chi-restraints excluded: chain V residue 311 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain W residue 65 LYS Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 294 GLU Chi-restraints excluded: chain W residue 395 GLU Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 294 GLU Chi-restraints excluded: chain X residue 395 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 478 optimal weight: 0.9990 chunk 318 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 585 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 160 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 376 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 182 GLN W 218 GLN ** X 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.064144 restraints weight = 116531.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.066646 restraints weight = 58059.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.068281 restraints weight = 37587.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.069367 restraints weight = 28421.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.070073 restraints weight = 23713.876| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48816 Z= 0.118 Angle : 0.599 10.281 65844 Z= 0.314 Chirality : 0.040 0.174 7296 Planarity : 0.003 0.046 8544 Dihedral : 3.669 20.108 6588 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.80 % Allowed : 4.42 % Favored : 94.78 % Rotamer: Outliers : 2.10 % Allowed : 24.85 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.11), residues: 6000 helix: 2.94 (0.10), residues: 2892 sheet: -0.75 (0.23), residues: 528 loop : -1.09 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 78 TYR 0.009 0.001 TYR V 77 PHE 0.014 0.001 PHE S 338 TRP 0.008 0.001 TRP N 89 HIS 0.004 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00266 (48816) covalent geometry : angle 0.59923 (65844) hydrogen bonds : bond 0.03218 ( 2400) hydrogen bonds : angle 3.96635 ( 7056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1082 time to evaluate : 1.180 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: B 11 GLU cc_start: 0.9092 (tp30) cc_final: 0.8470 (tp30) REVERT: B 33 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8269 (mp0) REVERT: B 71 GLU cc_start: 0.8325 (mp0) cc_final: 0.7867 (mp0) REVERT: M 79 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8997 (mp) REVERT: M 183 ASN cc_start: 0.9122 (t0) cc_final: 0.8733 (t0) REVERT: M 301 ASN cc_start: 0.8406 (t0) cc_final: 0.8196 (t0) REVERT: M 359 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8394 (pt0) REVERT: A 33 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8408 (mt-10) REVERT: A 71 GLU cc_start: 0.8357 (mp0) cc_final: 0.8022 (mp0) REVERT: A 82 SER cc_start: 0.9158 (p) cc_final: 0.8938 (p) REVERT: N 145 GLU cc_start: 0.8822 (mp0) cc_final: 0.8247 (mp0) REVERT: N 157 MET cc_start: 0.9024 (mpp) cc_final: 0.8394 (mpp) REVERT: N 183 ASN cc_start: 0.9110 (t0) cc_final: 0.8476 (t0) REVERT: N 184 GLN cc_start: 0.8519 (mp10) cc_final: 0.8077 (mp10) REVERT: N 261 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: N 362 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8680 (mt-10) REVERT: N 398 LEU cc_start: 0.8572 (tp) cc_final: 0.8371 (tp) REVERT: C 71 GLU cc_start: 0.8428 (mp0) cc_final: 0.7791 (mp0) REVERT: O 52 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8694 (mt-10) REVERT: O 103 LYS cc_start: 0.7469 (ptpp) cc_final: 0.7262 (ptpp) REVERT: O 145 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8935 (mp0) REVERT: O 157 MET cc_start: 0.8913 (mpp) cc_final: 0.8467 (mpp) REVERT: O 183 ASN cc_start: 0.9128 (t0) cc_final: 0.8289 (t0) REVERT: O 326 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7359 (tm-30) REVERT: O 357 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8793 (mmmm) REVERT: O 359 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8594 (pt0) REVERT: D 11 GLU cc_start: 0.9093 (tp30) cc_final: 0.8821 (tp30) REVERT: D 71 GLU cc_start: 0.8582 (mp0) cc_final: 0.8174 (mp0) REVERT: D 82 SER cc_start: 0.9166 (p) cc_final: 0.8951 (p) REVERT: D 104 MET cc_start: 0.8809 (ptm) cc_final: 0.8474 (ppp) REVERT: P 68 LYS cc_start: 0.9255 (tppt) cc_final: 0.8951 (tppt) REVERT: P 79 LEU cc_start: 0.9240 (mp) cc_final: 0.8962 (mp) REVERT: P 145 GLU cc_start: 0.8527 (mp0) cc_final: 0.8092 (mp0) REVERT: P 157 MET cc_start: 0.8812 (mpp) cc_final: 0.8402 (mpp) REVERT: P 183 ASN cc_start: 0.9111 (t0) cc_final: 0.8472 (t0) REVERT: P 184 GLN cc_start: 0.8518 (mp10) cc_final: 0.8075 (mp10) REVERT: P 261 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: P 359 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8382 (mt-10) REVERT: P 362 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8951 (mt-10) REVERT: P 397 LYS cc_start: 0.9250 (mmmm) cc_final: 0.9000 (mmtp) REVERT: E 11 GLU cc_start: 0.9078 (tp30) cc_final: 0.8647 (tp30) REVERT: E 15 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8809 (ttmm) REVERT: E 33 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8194 (mp0) REVERT: E 71 GLU cc_start: 0.8357 (mp0) cc_final: 0.7806 (mp0) REVERT: Q 183 ASN cc_start: 0.9122 (t0) cc_final: 0.8726 (t0) REVERT: Q 301 ASN cc_start: 0.8397 (t0) cc_final: 0.8173 (t0) REVERT: Q 359 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8382 (pt0) REVERT: Q 398 LEU cc_start: 0.8671 (tp) cc_final: 0.8377 (tp) REVERT: F 70 ASP cc_start: 0.8296 (p0) cc_final: 0.8036 (p0) REVERT: F 71 GLU cc_start: 0.8518 (mp0) cc_final: 0.7931 (mp0) REVERT: F 74 GLU cc_start: 0.8326 (tp30) cc_final: 0.7808 (tp30) REVERT: F 78 ARG cc_start: 0.8829 (ptt90) cc_final: 0.8593 (ptt90) REVERT: F 120 ARG cc_start: 0.8837 (tpt-90) cc_final: 0.8448 (ttt-90) REVERT: R 68 LYS cc_start: 0.9289 (tppt) cc_final: 0.8922 (tppt) REVERT: R 145 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8939 (mp0) REVERT: R 157 MET cc_start: 0.8928 (mpp) cc_final: 0.8459 (mpp) REVERT: R 183 ASN cc_start: 0.9114 (t0) cc_final: 0.8237 (t0) REVERT: R 230 CYS cc_start: 0.8399 (m) cc_final: 0.8151 (t) REVERT: R 326 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7212 (tm-30) REVERT: R 359 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8560 (pt0) REVERT: G 11 GLU cc_start: 0.9141 (tp30) cc_final: 0.8909 (tp30) REVERT: G 33 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8460 (mt-10) REVERT: G 88 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8535 (mm-30) REVERT: S 68 LYS cc_start: 0.9262 (tppt) cc_final: 0.8972 (tppt) REVERT: S 145 GLU cc_start: 0.8614 (mp0) cc_final: 0.8092 (mp0) REVERT: S 157 MET cc_start: 0.8843 (mpp) cc_final: 0.8433 (mpp) REVERT: S 183 ASN cc_start: 0.9109 (t0) cc_final: 0.8470 (t0) REVERT: S 184 GLN cc_start: 0.8533 (mp10) cc_final: 0.8094 (mp10) REVERT: S 261 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: S 359 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8438 (mt-10) REVERT: S 398 LEU cc_start: 0.8883 (tp) cc_final: 0.8640 (tp) REVERT: H 11 GLU cc_start: 0.9086 (tp30) cc_final: 0.8050 (tp30) REVERT: H 15 LYS cc_start: 0.9113 (mtmm) cc_final: 0.7485 (mtmm) REVERT: H 33 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8264 (mp0) REVERT: H 71 GLU cc_start: 0.8040 (mp0) cc_final: 0.7811 (mp0) REVERT: H 72 ASP cc_start: 0.8672 (p0) cc_final: 0.8431 (p0) REVERT: H 75 SER cc_start: 0.9462 (p) cc_final: 0.9219 (p) REVERT: H 105 MET cc_start: 0.8439 (mtp) cc_final: 0.7801 (mmt) REVERT: T 79 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9010 (mp) REVERT: T 183 ASN cc_start: 0.9125 (t0) cc_final: 0.8727 (t0) REVERT: T 301 ASN cc_start: 0.8664 (t0) cc_final: 0.8337 (t0) REVERT: T 359 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8389 (pt0) REVERT: T 398 LEU cc_start: 0.8715 (tp) cc_final: 0.8431 (tp) REVERT: I 11 GLU cc_start: 0.9247 (tp30) cc_final: 0.8914 (tp30) REVERT: I 33 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8569 (mt-10) REVERT: I 71 GLU cc_start: 0.8561 (mp0) cc_final: 0.7986 (mp0) REVERT: I 74 GLU cc_start: 0.8559 (tp30) cc_final: 0.8230 (tp30) REVERT: U 54 MET cc_start: 0.8833 (mtm) cc_final: 0.8592 (mtm) REVERT: U 68 LYS cc_start: 0.9272 (tppt) cc_final: 0.8977 (tppt) REVERT: U 103 LYS cc_start: 0.7199 (ptpp) cc_final: 0.6955 (ptpp) REVERT: U 145 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8848 (mp0) REVERT: U 157 MET cc_start: 0.8929 (mpp) cc_final: 0.8433 (mpp) REVERT: U 183 ASN cc_start: 0.9101 (t0) cc_final: 0.8218 (t0) REVERT: U 230 CYS cc_start: 0.8398 (m) cc_final: 0.8132 (t) REVERT: U 326 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7185 (tm-30) REVERT: U 359 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8492 (pt0) REVERT: J 11 GLU cc_start: 0.9115 (tp30) cc_final: 0.8837 (tp30) REVERT: J 71 GLU cc_start: 0.8447 (mp0) cc_final: 0.8065 (mp0) REVERT: J 82 SER cc_start: 0.9170 (p) cc_final: 0.8955 (p) REVERT: V 104 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7059 (t70) REVERT: V 145 GLU cc_start: 0.8762 (mp0) cc_final: 0.8386 (mp0) REVERT: V 157 MET cc_start: 0.8790 (mpp) cc_final: 0.8145 (mpp) REVERT: V 183 ASN cc_start: 0.9113 (t0) cc_final: 0.8478 (t0) REVERT: V 184 GLN cc_start: 0.8534 (mp10) cc_final: 0.8096 (mp10) REVERT: V 261 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: V 323 LYS cc_start: 0.9478 (mmtt) cc_final: 0.9174 (mmmt) REVERT: V 357 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8223 (mtmm) REVERT: V 362 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8404 (mt-10) REVERT: K 11 GLU cc_start: 0.9075 (tp30) cc_final: 0.8595 (tp30) REVERT: K 15 LYS cc_start: 0.9125 (mtmm) cc_final: 0.8775 (ttmm) REVERT: K 33 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8276 (mp0) REVERT: K 72 ASP cc_start: 0.8685 (p0) cc_final: 0.8468 (p0) REVERT: K 75 SER cc_start: 0.9490 (p) cc_final: 0.9281 (p) REVERT: W 183 ASN cc_start: 0.9126 (t0) cc_final: 0.8730 (t0) REVERT: W 301 ASN cc_start: 0.8558 (t0) cc_final: 0.8302 (t0) REVERT: W 359 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8370 (pt0) REVERT: W 398 LEU cc_start: 0.8665 (tp) cc_final: 0.8431 (tp) REVERT: L 45 LYS cc_start: 0.9428 (mttp) cc_final: 0.9084 (mttm) REVERT: L 70 ASP cc_start: 0.8611 (p0) cc_final: 0.8255 (p0) REVERT: L 71 GLU cc_start: 0.8647 (mp0) cc_final: 0.8092 (mp0) REVERT: L 78 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7900 (ptt90) REVERT: X 157 MET cc_start: 0.8921 (mpp) cc_final: 0.8484 (mpp) REVERT: X 326 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7201 (tm-30) outliers start: 109 outliers final: 75 residues processed: 1154 average time/residue: 0.1908 time to fit residues: 359.5245 Evaluate side-chains 1129 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1046 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain O residue 395 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 261 GLU Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain P residue 275 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain Q residue 65 LYS Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain Q residue 272 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 395 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 178 GLN Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 74 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain T residue 65 LYS Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 272 ILE Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 178 GLN Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 272 ILE Chi-restraints excluded: chain V residue 275 VAL Chi-restraints excluded: chain V residue 311 THR Chi-restraints excluded: chain V residue 357 LYS Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 294 GLU Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 294 GLU Chi-restraints excluded: chain X residue 395 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 154 optimal weight: 6.9990 chunk 313 optimal weight: 4.9990 chunk 577 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 579 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 547 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 422 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN J 91 GLN V 217 GLN ** X 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.086167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.063190 restraints weight = 117499.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.065670 restraints weight = 58709.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.067292 restraints weight = 38088.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.068384 restraints weight = 28817.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.069079 restraints weight = 24064.354| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 48816 Z= 0.135 Angle : 0.616 9.906 65844 Z= 0.323 Chirality : 0.040 0.184 7296 Planarity : 0.003 0.046 8544 Dihedral : 3.668 20.307 6588 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.80 % Allowed : 4.95 % Favored : 94.25 % Rotamer: Outliers : 1.75 % Allowed : 25.23 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.11), residues: 6000 helix: 2.91 (0.10), residues: 2892 sheet: -0.71 (0.23), residues: 528 loop : -1.07 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 78 TYR 0.009 0.001 TYR L 48 PHE 0.011 0.001 PHE S 338 TRP 0.007 0.001 TRP Q 89 HIS 0.003 0.000 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00314 (48816) covalent geometry : angle 0.61581 (65844) hydrogen bonds : bond 0.03593 ( 2400) hydrogen bonds : angle 3.99942 ( 7056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12000 Ramachandran restraints generated. 6000 Oldfield, 0 Emsley, 6000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1040 time to evaluate : 1.223 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: B 11 GLU cc_start: 0.9095 (tp30) cc_final: 0.8484 (tp30) REVERT: B 33 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8279 (mp0) REVERT: B 71 GLU cc_start: 0.8206 (mp0) cc_final: 0.7909 (mp0) REVERT: M 79 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9020 (mp) REVERT: M 183 ASN cc_start: 0.9145 (t0) cc_final: 0.8760 (t0) REVERT: M 359 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8400 (pt0) REVERT: M 398 LEU cc_start: 0.8598 (tp) cc_final: 0.8202 (tp) REVERT: A 70 ASP cc_start: 0.8982 (p0) cc_final: 0.8602 (p0) REVERT: A 71 GLU cc_start: 0.8381 (mp0) cc_final: 0.8017 (mp0) REVERT: A 82 SER cc_start: 0.9173 (p) cc_final: 0.8958 (p) REVERT: A 104 MET cc_start: 0.8725 (ptm) cc_final: 0.8507 (ptm) REVERT: N 145 GLU cc_start: 0.8799 (mp0) cc_final: 0.8272 (mp0) REVERT: N 157 MET cc_start: 0.9046 (mpp) cc_final: 0.8400 (mpp) REVERT: N 183 ASN cc_start: 0.9127 (t0) cc_final: 0.8492 (t0) REVERT: N 184 GLN cc_start: 0.8530 (mp10) cc_final: 0.8091 (mp10) REVERT: N 261 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8176 (pt0) REVERT: N 362 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8676 (mt-10) REVERT: C 71 GLU cc_start: 0.8437 (mp0) cc_final: 0.7802 (mp0) REVERT: O 52 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8697 (mt-10) REVERT: O 145 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8948 (mp0) REVERT: O 157 MET cc_start: 0.8942 (mpp) cc_final: 0.8489 (mpp) REVERT: O 183 ASN cc_start: 0.9157 (t0) cc_final: 0.8294 (t0) REVERT: O 326 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7101 (tm-30) REVERT: O 359 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8489 (pt0) REVERT: O 362 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8790 (mt-10) REVERT: D 11 GLU cc_start: 0.9109 (tp30) cc_final: 0.8836 (tp30) REVERT: D 82 SER cc_start: 0.9185 (p) cc_final: 0.8963 (p) REVERT: P 68 LYS cc_start: 0.9291 (tppt) cc_final: 0.8994 (tppt) REVERT: P 79 LEU cc_start: 0.9253 (mp) cc_final: 0.8977 (mp) REVERT: P 145 GLU cc_start: 0.8539 (mp0) cc_final: 0.8102 (mp0) REVERT: P 157 MET cc_start: 0.8932 (mpp) cc_final: 0.8527 (mpp) REVERT: P 183 ASN cc_start: 0.9129 (t0) cc_final: 0.8489 (t0) REVERT: P 184 GLN cc_start: 0.8532 (mp10) cc_final: 0.8092 (mp10) REVERT: P 261 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: P 359 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8380 (mt-10) REVERT: P 362 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8903 (mt-10) REVERT: P 397 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8989 (mmtp) REVERT: E 11 GLU cc_start: 0.9086 (tp30) cc_final: 0.8686 (tp30) REVERT: E 15 LYS cc_start: 0.9158 (mtmm) cc_final: 0.8876 (ttmm) REVERT: E 33 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8206 (mp0) REVERT: E 71 GLU cc_start: 0.8344 (mp0) cc_final: 0.7660 (mp0) REVERT: Q 183 ASN cc_start: 0.9148 (t0) cc_final: 0.8756 (t0) REVERT: Q 359 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8380 (pt0) REVERT: Q 398 LEU cc_start: 0.8689 (tp) cc_final: 0.8395 (tp) REVERT: F 70 ASP cc_start: 0.8286 (p0) cc_final: 0.8043 (p0) REVERT: F 71 GLU cc_start: 0.8527 (mp0) cc_final: 0.7925 (mp0) REVERT: F 74 GLU cc_start: 0.8358 (tp30) cc_final: 0.7845 (tp30) REVERT: F 78 ARG cc_start: 0.8847 (ptt90) cc_final: 0.8612 (ptt90) REVERT: F 120 ARG cc_start: 0.8827 (tpt-90) cc_final: 0.8441 (ttt-90) REVERT: R 145 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8946 (mp0) REVERT: R 157 MET cc_start: 0.8957 (mpp) cc_final: 0.8474 (mpp) REVERT: R 183 ASN cc_start: 0.9160 (t0) cc_final: 0.8302 (t0) REVERT: R 230 CYS cc_start: 0.8396 (m) cc_final: 0.8171 (t) REVERT: R 326 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7220 (tm-30) REVERT: G 11 GLU cc_start: 0.9153 (tp30) cc_final: 0.8927 (tp30) REVERT: G 71 GLU cc_start: 0.8362 (mp0) cc_final: 0.8101 (mp0) REVERT: G 88 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8555 (mm-30) REVERT: S 68 LYS cc_start: 0.9287 (tppt) cc_final: 0.8989 (tppt) REVERT: S 145 GLU cc_start: 0.8557 (mp0) cc_final: 0.8028 (mp0) REVERT: S 157 MET cc_start: 0.8900 (mpp) cc_final: 0.8484 (mpp) REVERT: S 183 ASN cc_start: 0.9123 (t0) cc_final: 0.8486 (t0) REVERT: S 184 GLN cc_start: 0.8539 (mp10) cc_final: 0.8099 (mp10) REVERT: S 261 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8176 (pt0) REVERT: S 359 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8410 (mt-10) REVERT: H 11 GLU cc_start: 0.9090 (tp30) cc_final: 0.8664 (tp30) REVERT: H 15 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8842 (ttmm) REVERT: H 33 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8238 (mp0) REVERT: H 72 ASP cc_start: 0.8701 (p0) cc_final: 0.8466 (p0) REVERT: H 75 SER cc_start: 0.9484 (p) cc_final: 0.9242 (p) REVERT: T 79 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9045 (mp) REVERT: T 182 GLN cc_start: 0.8581 (mt0) cc_final: 0.8235 (mp10) REVERT: T 183 ASN cc_start: 0.9149 (t0) cc_final: 0.8752 (t0) REVERT: T 301 ASN cc_start: 0.8666 (t0) cc_final: 0.8315 (t0) REVERT: T 359 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8378 (pt0) REVERT: T 398 LEU cc_start: 0.8593 (tp) cc_final: 0.8320 (tp) REVERT: I 11 GLU cc_start: 0.9262 (tp30) cc_final: 0.8905 (tp30) REVERT: I 33 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8578 (mt-10) REVERT: I 70 ASP cc_start: 0.8662 (p0) cc_final: 0.8258 (p0) REVERT: I 71 GLU cc_start: 0.8539 (mp0) cc_final: 0.7902 (mp0) REVERT: I 74 GLU cc_start: 0.8566 (tp30) cc_final: 0.8234 (tp30) REVERT: U 52 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8710 (mt-10) REVERT: U 54 MET cc_start: 0.8856 (mtm) cc_final: 0.8625 (mtm) REVERT: U 145 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8890 (mp0) REVERT: U 157 MET cc_start: 0.8952 (mpp) cc_final: 0.8491 (mpp) REVERT: U 183 ASN cc_start: 0.9146 (t0) cc_final: 0.8285 (t0) REVERT: U 230 CYS cc_start: 0.8385 (m) cc_final: 0.8156 (t) REVERT: U 326 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7243 (tm-30) REVERT: J 3 GLN cc_start: 0.8526 (tp40) cc_final: 0.8310 (tp40) REVERT: J 11 GLU cc_start: 0.9122 (tp30) cc_final: 0.8862 (tp30) REVERT: J 71 GLU cc_start: 0.8497 (mp0) cc_final: 0.8105 (mp0) REVERT: J 82 SER cc_start: 0.9185 (p) cc_final: 0.8961 (p) REVERT: V 104 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7041 (t70) REVERT: V 145 GLU cc_start: 0.8778 (mp0) cc_final: 0.8361 (mp0) REVERT: V 157 MET cc_start: 0.9053 (mpp) cc_final: 0.8420 (mpp) REVERT: V 183 ASN cc_start: 0.9124 (t0) cc_final: 0.8489 (t0) REVERT: V 184 GLN cc_start: 0.8539 (mp10) cc_final: 0.8100 (mp10) REVERT: V 261 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8217 (pt0) REVERT: V 323 LYS cc_start: 0.9492 (mmtt) cc_final: 0.9205 (mmmt) REVERT: K 11 GLU cc_start: 0.9074 (tp30) cc_final: 0.8647 (tp30) REVERT: K 15 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8843 (ttmm) REVERT: K 33 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8283 (mp0) REVERT: W 183 ASN cc_start: 0.9148 (t0) cc_final: 0.8757 (t0) REVERT: W 301 ASN cc_start: 0.8617 (t0) cc_final: 0.8348 (t0) REVERT: W 398 LEU cc_start: 0.8704 (tp) cc_final: 0.8458 (tp) REVERT: L 45 LYS cc_start: 0.9432 (mttp) cc_final: 0.9090 (mttm) REVERT: L 70 ASP cc_start: 0.8627 (p0) cc_final: 0.8236 (p0) REVERT: L 71 GLU cc_start: 0.8621 (mp0) cc_final: 0.8063 (mp0) REVERT: X 145 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8816 (mp0) REVERT: X 157 MET cc_start: 0.8951 (mpp) cc_final: 0.8506 (mpp) REVERT: X 326 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7222 (tm-30) REVERT: X 359 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8504 (pt0) outliers start: 91 outliers final: 74 residues processed: 1109 average time/residue: 0.1884 time to fit residues: 342.1622 Evaluate side-chains 1106 residues out of total 5196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1025 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain N residue 261 GLU Chi-restraints excluded: chain N residue 272 ILE Chi-restraints excluded: chain N residue 275 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain O residue 294 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 261 GLU Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain P residue 275 VAL Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain Q residue 65 LYS Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain Q residue 272 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain R residue 99 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 315 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 272 ILE Chi-restraints excluded: chain S residue 275 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 134 ARG Chi-restraints excluded: chain T residue 272 ILE Chi-restraints excluded: chain T residue 311 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain U residue 294 GLU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain V residue 178 GLN Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 261 GLU Chi-restraints excluded: chain V residue 272 ILE Chi-restraints excluded: chain V residue 275 VAL Chi-restraints excluded: chain V residue 311 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 129 THR Chi-restraints excluded: chain W residue 134 ARG Chi-restraints excluded: chain W residue 294 GLU Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain X residue 99 VAL Chi-restraints excluded: chain X residue 294 GLU Chi-restraints excluded: chain X residue 395 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 347 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 254 optimal weight: 0.5980 chunk 304 optimal weight: 5.9990 chunk 458 optimal weight: 10.0000 chunk 409 optimal weight: 7.9990 chunk 462 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 417 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 217 GLN D 91 GLN F 99 ASN J 91 GLN V 217 GLN ** X 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.085127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.062139 restraints weight = 117292.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.064590 restraints weight = 58806.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.066188 restraints weight = 38236.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.067261 restraints weight = 28994.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.067957 restraints weight = 24245.612| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48816 Z= 0.155 Angle : 0.627 9.612 65844 Z= 0.331 Chirality : 0.041 0.202 7296 Planarity : 0.004 0.044 8544 Dihedral : 3.728 21.297 6588 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.80 % Allowed : 4.88 % Favored : 94.32 % Rotamer: Outliers : 1.96 % Allowed : 25.10 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.11), residues: 6000 helix: 2.89 (0.10), residues: 2892 sheet: -0.72 (0.23), residues: 528 loop : -1.16 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 78 TYR 0.014 0.001 TYR L 48 PHE 0.010 0.001 PHE S 338 TRP 0.007 0.001 TRP Q 89 HIS 0.003 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00364 (48816) covalent geometry : angle 0.62747 (65844) hydrogen bonds : bond 0.04043 ( 2400) hydrogen bonds : angle 4.09968 ( 7056) =============================================================================== Job complete usr+sys time: 8450.12 seconds wall clock time: 145 minutes 54.56 seconds (8754.56 seconds total)