Starting phenix.real_space_refine on Tue Aug 26 19:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8php_17670/08_2025/8php_17670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8php_17670/08_2025/8php_17670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8php_17670/08_2025/8php_17670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8php_17670/08_2025/8php_17670.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8php_17670/08_2025/8php_17670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8php_17670/08_2025/8php_17670.map" } resolution = 2.56 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 108 5.16 5 C 26352 2.51 5 N 6708 2.21 5 O 7644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s 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: 40812 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "B" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 3.11, per 1000 atoms: 0.08 Number of scatterers: 40812 At special positions: 0 Unit cell: (199.23, 199.23, 120.872, 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 108 16.00 O 7644 8.00 N 6708 7.00 C 26352 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: 2.24 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9576 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 60 sheets defined 60.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 163 through 184 removed outlier: 4.418A pdb=" N TYR A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 285 through 303 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 389 Processing helix chain 'A' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 92 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 109 through 126 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 145 through 163 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 285 through 303 Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 389 Processing helix chain 'C' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 92 Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 109 through 126 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 145 through 163 Processing helix chain 'E' and resid 14 through 22 Processing helix chain 'E' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL E 32 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR E 177 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 266 Processing helix chain 'E' and resid 285 through 303 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 327 through 353 removed outlier: 4.311A pdb=" N LYS E 347 " --> pdb=" O SER E 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 389 Processing helix chain 'E' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 403 " --> pdb=" O MET E 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 92 Processing helix chain 'F' and resid 95 through 98 Processing helix chain 'F' and resid 99 through 107 Processing helix chain 'F' and resid 109 through 126 Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 145 through 163 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL G 32 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 163 through 184 removed outlier: 4.418A pdb=" N TYR G 177 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 266 Processing helix chain 'G' and resid 285 through 303 Processing helix chain 'G' and resid 305 through 311 Processing helix chain 'G' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS G 347 " --> pdb=" O SER G 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS G 350 " --> pdb=" O LEU G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 389 Processing helix chain 'G' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS G 401 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS G 403 " --> pdb=" O MET G 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 92 Processing helix chain 'H' and resid 95 through 98 Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 109 through 126 Processing helix chain 'H' and resid 127 through 135 Processing helix chain 'H' and resid 145 through 163 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL I 32 " --> pdb=" O TYR I 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 37 " --> pdb=" O ALA I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'I' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR I 177 " --> pdb=" O PHE I 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG I 183 " --> pdb=" O GLU I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 266 Processing helix chain 'I' and resid 285 through 303 Processing helix chain 'I' and resid 305 through 311 Processing helix chain 'I' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS I 347 " --> pdb=" O SER I 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR I 349 " --> pdb=" O ASN I 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 389 Processing helix chain 'I' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS I 401 " --> pdb=" O LEU I 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU I 402 " --> pdb=" O ALA I 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS I 403 " --> pdb=" O MET I 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 92 Processing helix chain 'J' and resid 95 through 98 Processing helix chain 'J' and resid 99 through 107 Processing helix chain 'J' and resid 109 through 126 Processing helix chain 'J' and resid 127 through 135 Processing helix chain 'J' and resid 145 through 163 Processing helix chain 'K' and resid 14 through 22 Processing helix chain 'K' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL K 32 " --> pdb=" O TYR K 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN K 68 " --> pdb=" O ASN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG K 183 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 266 Processing helix chain 'K' and resid 285 through 303 Processing helix chain 'K' and resid 305 through 311 Processing helix chain 'K' and resid 327 through 353 removed outlier: 4.311A pdb=" N LYS K 347 " --> pdb=" O SER K 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR K 349 " --> pdb=" O ASN K 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS K 350 " --> pdb=" O LEU K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 389 Processing helix chain 'K' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU K 402 " --> pdb=" O ALA K 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 403 " --> pdb=" O MET K 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 92 Processing helix chain 'L' and resid 95 through 98 Processing helix chain 'L' and resid 99 through 107 Processing helix chain 'L' and resid 109 through 126 Processing helix chain 'L' and resid 127 through 135 Processing helix chain 'L' and resid 145 through 163 Processing helix chain 'M' and resid 14 through 22 Processing helix chain 'M' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL M 32 " --> pdb=" O TYR M 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA M 33 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU M 37 " --> pdb=" O ALA M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 110 No H-bonds generated for 'chain 'M' and resid 108 through 110' Processing helix chain 'M' and resid 163 through 184 removed outlier: 4.418A pdb=" N TYR M 177 " --> pdb=" O PHE M 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 266 Processing helix chain 'M' and resid 285 through 303 Processing helix chain 'M' and resid 305 through 311 Processing helix chain 'M' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS M 347 " --> pdb=" O SER M 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR M 349 " --> pdb=" O ASN M 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS M 350 " --> pdb=" O LEU M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 389 Processing helix chain 'M' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS M 401 " --> pdb=" O LEU M 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU M 402 " --> pdb=" O ALA M 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS M 403 " --> pdb=" O MET M 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 92 Processing helix chain 'N' and resid 95 through 98 Processing helix chain 'N' and resid 99 through 107 Processing helix chain 'N' and resid 109 through 126 Processing helix chain 'N' and resid 127 through 135 Processing helix chain 'N' and resid 145 through 163 Processing helix chain 'O' and resid 14 through 22 Processing helix chain 'O' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL O 32 " --> pdb=" O TYR O 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA O 33 " --> pdb=" O ILE O 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 110 No H-bonds generated for 'chain 'O' and resid 108 through 110' Processing helix chain 'O' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR O 177 " --> pdb=" O PHE O 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG O 183 " --> pdb=" O GLU O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 266 Processing helix chain 'O' and resid 285 through 303 Processing helix chain 'O' and resid 305 through 311 Processing helix chain 'O' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS O 347 " --> pdb=" O SER O 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR O 349 " --> pdb=" O ASN O 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS O 350 " --> pdb=" O LEU O 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 365 through 389 Processing helix chain 'O' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS O 401 " --> pdb=" O LEU O 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU O 402 " --> pdb=" O ALA O 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS O 403 " --> pdb=" O MET O 399 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 92 Processing helix chain 'P' and resid 95 through 98 Processing helix chain 'P' and resid 99 through 107 Processing helix chain 'P' and resid 109 through 126 Processing helix chain 'P' and resid 127 through 135 Processing helix chain 'P' and resid 145 through 163 Processing helix chain 'Q' and resid 14 through 22 Processing helix chain 'Q' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL Q 32 " --> pdb=" O TYR Q 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA Q 33 " --> pdb=" O ILE Q 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU Q 37 " --> pdb=" O ALA Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing helix chain 'Q' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR Q 177 " --> pdb=" O PHE Q 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG Q 183 " --> pdb=" O GLU Q 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 266 Processing helix chain 'Q' and resid 285 through 303 Processing helix chain 'Q' and resid 305 through 311 Processing helix chain 'Q' and resid 327 through 353 removed outlier: 4.311A pdb=" N LYS Q 347 " --> pdb=" O SER Q 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR Q 349 " --> pdb=" O ASN Q 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS Q 350 " --> pdb=" O LEU Q 346 " (cutoff:3.500A) Processing helix chain 'Q' and resid 365 through 389 Processing helix chain 'Q' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS Q 401 " --> pdb=" O LEU Q 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU Q 402 " --> pdb=" O ALA Q 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS Q 403 " --> pdb=" O MET Q 399 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 92 Processing helix chain 'R' and resid 95 through 98 Processing helix chain 'R' and resid 99 through 107 Processing helix chain 'R' and resid 109 through 126 Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 145 through 163 Processing helix chain 'S' and resid 14 through 22 Processing helix chain 'S' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL S 32 " --> pdb=" O TYR S 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA S 33 " --> pdb=" O ILE S 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU S 37 " --> pdb=" O ALA S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN S 68 " --> pdb=" O ASN S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 110 No H-bonds generated for 'chain 'S' and resid 108 through 110' Processing helix chain 'S' and resid 163 through 184 removed outlier: 4.418A pdb=" N TYR S 177 " --> pdb=" O PHE S 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG S 183 " --> pdb=" O GLU S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 258 through 266 Processing helix chain 'S' and resid 285 through 303 Processing helix chain 'S' and resid 305 through 311 Processing helix chain 'S' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS S 347 " --> pdb=" O SER S 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR S 349 " --> pdb=" O ASN S 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS S 350 " --> pdb=" O LEU S 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 365 through 389 Processing helix chain 'S' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS S 401 " --> pdb=" O LEU S 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU S 402 " --> pdb=" O ALA S 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS S 403 " --> pdb=" O MET S 399 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 92 Processing helix chain 'T' and resid 95 through 98 Processing helix chain 'T' and resid 99 through 107 Processing helix chain 'T' and resid 109 through 126 Processing helix chain 'T' and resid 127 through 135 Processing helix chain 'T' and resid 145 through 163 Processing helix chain 'U' and resid 14 through 22 Processing helix chain 'U' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL U 32 " --> pdb=" O TYR U 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA U 33 " --> pdb=" O ILE U 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU U 37 " --> pdb=" O ALA U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR U 177 " --> pdb=" O PHE U 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG U 183 " --> pdb=" O GLU U 179 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 266 Processing helix chain 'U' and resid 285 through 303 Processing helix chain 'U' and resid 305 through 311 Processing helix chain 'U' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS U 347 " --> pdb=" O SER U 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR U 349 " --> pdb=" O ASN U 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS U 350 " --> pdb=" O LEU U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 365 through 389 Processing helix chain 'U' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS U 401 " --> pdb=" O LEU U 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU U 402 " --> pdb=" O ALA U 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS U 403 " --> pdb=" O MET U 399 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 92 Processing helix chain 'V' and resid 95 through 98 Processing helix chain 'V' and resid 99 through 107 Processing helix chain 'V' and resid 109 through 126 Processing helix chain 'V' and resid 127 through 135 Processing helix chain 'V' and resid 145 through 163 Processing helix chain 'W' and resid 14 through 22 Processing helix chain 'W' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA W 33 " --> pdb=" O ILE W 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN W 68 " --> pdb=" O ASN W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 110 No H-bonds generated for 'chain 'W' and resid 108 through 110' Processing helix chain 'W' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR W 177 " --> pdb=" O PHE W 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG W 183 " --> pdb=" O GLU W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 258 through 266 Processing helix chain 'W' and resid 285 through 303 Processing helix chain 'W' and resid 305 through 311 Processing helix chain 'W' and resid 327 through 353 removed outlier: 4.311A pdb=" N LYS W 347 " --> pdb=" O SER W 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR W 349 " --> pdb=" O ASN W 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS W 350 " --> pdb=" O LEU W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 365 through 389 Processing helix chain 'W' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS W 401 " --> pdb=" O LEU W 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU W 402 " --> pdb=" O ALA W 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS W 403 " --> pdb=" O MET W 399 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 92 Processing helix chain 'X' and resid 95 through 98 Processing helix chain 'X' and resid 99 through 107 Processing helix chain 'X' and resid 109 through 126 Processing helix chain 'X' and resid 127 through 135 Processing helix chain 'X' and resid 145 through 163 Processing sheet with id=1, first strand: chain 'A' and resid 41 through 45 Processing sheet with id=2, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR A 80 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=4, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=5, first strand: chain 'A' and resid 188 through 193 Processing sheet with id=6, first strand: chain 'C' and resid 41 through 45 Processing sheet with id=7, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR C 80 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=9, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=10, first strand: chain 'C' and resid 188 through 193 Processing sheet with id=11, first strand: chain 'E' and resid 41 through 45 Processing sheet with id=12, first strand: chain 'E' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR E 80 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'E' and resid 112 through 113 Processing sheet with id=14, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=15, first strand: chain 'E' and resid 188 through 193 Processing sheet with id=16, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=17, first strand: chain 'G' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR G 80 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'G' and resid 112 through 113 Processing sheet with id=19, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=20, first strand: chain 'G' and resid 188 through 193 Processing sheet with id=21, first strand: chain 'I' and resid 41 through 45 Processing sheet with id=22, first strand: chain 'I' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR I 80 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'I' and resid 112 through 113 Processing sheet with id=24, first strand: chain 'I' and resid 151 through 152 Processing sheet with id=25, first strand: chain 'I' and resid 188 through 193 Processing sheet with id=26, first strand: chain 'K' and resid 41 through 45 Processing sheet with id=27, first strand: chain 'K' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR K 80 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'K' and resid 112 through 113 Processing sheet with id=29, first strand: chain 'K' and resid 151 through 152 Processing sheet with id=30, first strand: chain 'K' and resid 188 through 193 Processing sheet with id=31, first strand: chain 'M' and resid 41 through 45 Processing sheet with id=32, first strand: chain 'M' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR M 80 " --> pdb=" O LEU M 107 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'M' and resid 112 through 113 Processing sheet with id=34, first strand: chain 'M' and resid 151 through 152 Processing sheet with id=35, first strand: chain 'M' and resid 188 through 193 Processing sheet with id=36, first strand: chain 'O' and resid 41 through 45 Processing sheet with id=37, first strand: chain 'O' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR O 80 " --> pdb=" O LEU O 107 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'O' and resid 112 through 113 Processing sheet with id=39, first strand: chain 'O' and resid 151 through 152 Processing sheet with id=40, first strand: chain 'O' and resid 188 through 193 Processing sheet with id=41, first strand: chain 'Q' and resid 41 through 45 Processing sheet with id=42, first strand: chain 'Q' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR Q 80 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'Q' and resid 112 through 113 Processing sheet with id=44, first strand: chain 'Q' and resid 151 through 152 Processing sheet with id=45, first strand: chain 'Q' and resid 188 through 193 Processing sheet with id=46, first strand: chain 'S' and resid 41 through 45 Processing sheet with id=47, first strand: chain 'S' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR S 80 " --> pdb=" O LEU S 107 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'S' and resid 112 through 113 Processing sheet with id=49, first strand: chain 'S' and resid 151 through 152 Processing sheet with id=50, first strand: chain 'S' and resid 188 through 193 Processing sheet with id=51, first strand: chain 'U' and resid 41 through 45 Processing sheet with id=52, first strand: chain 'U' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR U 80 " --> pdb=" O LEU U 107 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'U' and resid 112 through 113 Processing sheet with id=54, first strand: chain 'U' and resid 151 through 152 Processing sheet with id=55, first strand: chain 'U' and resid 188 through 193 Processing sheet with id=56, first strand: chain 'W' and resid 41 through 45 Processing sheet with id=57, first strand: chain 'W' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR W 80 " --> pdb=" O LEU W 107 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'W' and resid 112 through 113 Processing sheet with id=59, first strand: chain 'W' and resid 151 through 152 Processing sheet with id=60, first strand: chain 'W' and resid 188 through 193 2388 hydrogen bonds defined for protein. 6984 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: 6.10 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13080 1.34 - 1.46: 8702 1.46 - 1.58: 19522 1.58 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 41472 Sorted by residual: bond pdb=" CA VAL F 126 " pdb=" CB VAL F 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 bond pdb=" CA VAL X 126 " pdb=" CB VAL X 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 bond pdb=" CA VAL R 126 " pdb=" CB VAL R 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 bond pdb=" CA VAL L 126 " pdb=" CB VAL L 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 bond pdb=" CA VAL D 126 " pdb=" CB VAL D 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 ... (remaining 41467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 54916 0.92 - 1.84: 668 1.84 - 2.76: 108 2.76 - 3.69: 36 3.69 - 4.61: 36 Bond angle restraints: 55764 Sorted by residual: angle pdb=" CG1 ILE X 143 " pdb=" CB ILE X 143 " pdb=" CG2 ILE X 143 " ideal model delta sigma weight residual 110.70 106.09 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CG1 ILE R 143 " pdb=" CB ILE R 143 " pdb=" CG2 ILE R 143 " ideal model delta sigma weight residual 110.70 106.09 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CG1 ILE L 143 " pdb=" CB ILE L 143 " pdb=" CG2 ILE L 143 " ideal model delta sigma weight residual 110.70 106.09 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CG1 ILE F 143 " pdb=" CB ILE F 143 " pdb=" CG2 ILE F 143 " ideal model delta sigma weight residual 110.70 106.09 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CG1 ILE J 143 " pdb=" CB ILE J 143 " pdb=" CG2 ILE J 143 " ideal model delta sigma weight residual 110.70 106.11 4.59 3.00e+00 1.11e-01 2.34e+00 ... (remaining 55759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 23256 16.51 - 33.02: 1608 33.02 - 49.53: 324 49.53 - 66.04: 156 66.04 - 82.55: 24 Dihedral angle restraints: 25368 sinusoidal: 10572 harmonic: 14796 Sorted by residual: dihedral pdb=" CB GLU E 266 " pdb=" CG GLU E 266 " pdb=" CD GLU E 266 " pdb=" OE1 GLU E 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.55 -82.55 1 3.00e+01 1.11e-03 9.28e+00 dihedral pdb=" CB GLU W 266 " pdb=" CG GLU W 266 " pdb=" CD GLU W 266 " pdb=" OE1 GLU W 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.55 -82.55 1 3.00e+01 1.11e-03 9.28e+00 dihedral pdb=" CB GLU Q 266 " pdb=" CG GLU Q 266 " pdb=" CD GLU Q 266 " pdb=" OE1 GLU Q 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.55 -82.55 1 3.00e+01 1.11e-03 9.28e+00 ... (remaining 25365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4286 0.027 - 0.053: 1236 0.053 - 0.080: 502 0.080 - 0.106: 120 0.106 - 0.133: 156 Chirality restraints: 6300 Sorted by residual: chirality pdb=" CB ILE V 140 " pdb=" CA ILE V 140 " pdb=" CG1 ILE V 140 " pdb=" CG2 ILE V 140 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB ILE P 140 " pdb=" CA ILE P 140 " pdb=" CG1 ILE P 140 " pdb=" CG2 ILE P 140 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB ILE D 140 " pdb=" CA ILE D 140 " pdb=" CG1 ILE D 140 " pdb=" CG2 ILE D 140 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 6297 not shown) Planarity restraints: 7032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 159 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO K 160 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO K 160 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO K 160 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 159 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO E 160 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 160 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 160 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Q 159 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO Q 160 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO Q 160 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO Q 160 " -0.017 5.00e-02 4.00e+02 ... (remaining 7029 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 13924 2.87 - 3.37: 38392 3.37 - 3.88: 67436 3.88 - 4.39: 78500 4.39 - 4.90: 130342 Nonbonded interactions: 328594 Sorted by model distance: nonbonded pdb=" OD2 ASP U 35 " pdb=" OH TYR U 329 " model vdw 2.357 3.040 nonbonded pdb=" OD2 ASP C 35 " pdb=" OH TYR C 329 " model vdw 2.357 3.040 nonbonded pdb=" OD2 ASP O 35 " pdb=" OH TYR O 329 " model vdw 2.357 3.040 nonbonded pdb=" OD2 ASP I 35 " pdb=" OH TYR I 329 " model vdw 2.357 3.040 nonbonded pdb=" OD2 ASP E 35 " pdb=" OH TYR E 329 " model vdw 2.357 3.040 ... (remaining 328589 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.860 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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:5.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.001 0.015 41472 Z= 0.065 Angle : 0.319 4.606 55764 Z= 0.174 Chirality : 0.036 0.133 6300 Planarity : 0.002 0.030 7032 Dihedral : 12.915 82.551 15792 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.55 (0.12), residues: 4872 helix: 1.70 (0.09), residues: 2916 sheet: -0.11 (0.22), residues: 624 loop : 0.29 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.010 0.001 TYR G 177 PHE 0.008 0.001 PHE A 189 HIS 0.004 0.001 HIS E 121 Details of bonding type rmsd covalent geometry : bond 0.00136 (41472) covalent geometry : angle 0.31858 (55764) hydrogen bonds : bond 0.23541 ( 2388) hydrogen bonds : angle 6.79600 ( 6984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 924 time to evaluate : 1.132 Fit side-chains REVERT: A 86 LYS cc_start: 0.8678 (tptt) cc_final: 0.8331 (tppp) REVERT: E 111 TYR cc_start: 0.9179 (m-10) cc_final: 0.8892 (m-80) REVERT: G 86 LYS cc_start: 0.8678 (tptt) cc_final: 0.8331 (tppp) REVERT: K 111 TYR cc_start: 0.9179 (m-10) cc_final: 0.8892 (m-80) REVERT: M 86 LYS cc_start: 0.8678 (tptt) cc_final: 0.8332 (tppp) REVERT: Q 111 TYR cc_start: 0.9179 (m-10) cc_final: 0.8892 (m-80) REVERT: S 86 LYS cc_start: 0.8678 (tptt) cc_final: 0.8331 (tppp) REVERT: W 111 TYR cc_start: 0.9179 (m-10) cc_final: 0.8892 (m-80) outliers start: 0 outliers final: 4 residues processed: 924 average time/residue: 0.7837 time to fit residues: 852.8269 Evaluate side-chains 552 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 548 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain S residue 118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 0.2980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 262 ASN A 314 GLN A 388 GLN B 96 ASN B 97 HIS C 48 HIS C 186 ASN C 262 ASN C 314 GLN C 385 GLN C 388 GLN D 97 HIS E 186 ASN E 314 GLN E 320 ASN E 388 GLN F 96 ASN F 97 HIS F 99 ASN G 186 ASN G 262 ASN G 314 GLN G 388 GLN H 96 ASN H 97 HIS I 48 HIS I 186 ASN I 262 ASN I 314 GLN I 385 GLN I 388 GLN J 97 HIS K 186 ASN K 314 GLN K 320 ASN K 388 GLN L 96 ASN L 97 HIS L 99 ASN M 186 ASN M 262 ASN M 314 GLN M 388 GLN N 96 ASN N 97 HIS O 48 HIS O 186 ASN O 262 ASN O 314 GLN O 385 GLN O 388 GLN P 97 HIS Q 186 ASN Q 314 GLN Q 320 ASN Q 388 GLN R 96 ASN R 97 HIS R 99 ASN S 186 ASN S 262 ASN S 314 GLN S 388 GLN T 96 ASN T 97 HIS U 48 HIS U 186 ASN U 262 ASN U 314 GLN U 385 GLN U 388 GLN V 97 HIS W 186 ASN W 314 GLN W 320 ASN W 388 GLN X 96 ASN X 97 HIS X 99 ASN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.072624 restraints weight = 62496.371| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.43 r_work: 0.2646 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41472 Z= 0.152 Angle : 0.520 8.247 55764 Z= 0.285 Chirality : 0.040 0.270 6300 Planarity : 0.004 0.026 7032 Dihedral : 3.986 44.870 5444 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.30 % Allowed : 8.16 % Favored : 89.54 % 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: 1.73 (0.12), residues: 4872 helix: 2.03 (0.10), residues: 2940 sheet: -0.26 (0.21), residues: 624 loop : -0.06 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 326 TYR 0.019 0.001 TYR U 177 PHE 0.017 0.002 PHE S 269 HIS 0.005 0.001 HIS U 121 Details of bonding type rmsd covalent geometry : bond 0.00340 (41472) covalent geometry : angle 0.52005 (55764) hydrogen bonds : bond 0.05987 ( 2388) hydrogen bonds : angle 4.69402 ( 6984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 628 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8705 (tptt) cc_final: 0.8313 (tppp) REVERT: A 99 GLU cc_start: 0.7838 (tt0) cc_final: 0.7579 (tt0) REVERT: A 338 GLU cc_start: 0.9121 (tt0) cc_final: 0.8851 (tt0) REVERT: A 339 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: A 385 GLN cc_start: 0.9074 (tt0) cc_final: 0.8466 (tm-30) REVERT: C 339 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8595 (mp-120) REVERT: E 99 GLU cc_start: 0.7888 (tt0) cc_final: 0.7610 (tt0) REVERT: E 110 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: E 339 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8521 (mp10) REVERT: E 385 GLN cc_start: 0.9033 (tt0) cc_final: 0.8401 (tm-30) REVERT: G 86 LYS cc_start: 0.8706 (tptt) cc_final: 0.8318 (tppp) REVERT: G 99 GLU cc_start: 0.7835 (tt0) cc_final: 0.7574 (tt0) REVERT: G 338 GLU cc_start: 0.9120 (tt0) cc_final: 0.8849 (tt0) REVERT: G 339 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8441 (mp10) REVERT: G 385 GLN cc_start: 0.9063 (tt0) cc_final: 0.8460 (tm-30) REVERT: I 339 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8588 (mp-120) REVERT: K 99 GLU cc_start: 0.7897 (tt0) cc_final: 0.7621 (tt0) REVERT: K 110 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: K 339 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: K 385 GLN cc_start: 0.9034 (tt0) cc_final: 0.8400 (tm-30) REVERT: M 86 LYS cc_start: 0.8709 (tptt) cc_final: 0.8315 (tppp) REVERT: M 99 GLU cc_start: 0.7838 (tt0) cc_final: 0.7578 (tt0) REVERT: M 338 GLU cc_start: 0.9130 (tt0) cc_final: 0.8861 (tt0) REVERT: M 339 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8432 (mp10) REVERT: M 385 GLN cc_start: 0.9066 (tt0) cc_final: 0.8462 (tm-30) REVERT: O 339 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8587 (mp-120) REVERT: Q 99 GLU cc_start: 0.7889 (tt0) cc_final: 0.7613 (tt0) REVERT: Q 110 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: Q 339 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: Q 385 GLN cc_start: 0.9036 (tt0) cc_final: 0.8402 (tm-30) REVERT: S 86 LYS cc_start: 0.8705 (tptt) cc_final: 0.8314 (tppp) REVERT: S 99 GLU cc_start: 0.7846 (tt0) cc_final: 0.7588 (tt0) REVERT: S 338 GLU cc_start: 0.9116 (tt0) cc_final: 0.8845 (tt0) REVERT: S 339 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8440 (mp10) REVERT: S 385 GLN cc_start: 0.9072 (tt0) cc_final: 0.8467 (tm-30) REVERT: U 339 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8596 (mp-120) REVERT: W 99 GLU cc_start: 0.7897 (tt0) cc_final: 0.7622 (tt0) REVERT: W 110 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: W 339 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8513 (mp10) REVERT: W 385 GLN cc_start: 0.9027 (tt0) cc_final: 0.8395 (tm-30) outliers start: 104 outliers final: 36 residues processed: 664 average time/residue: 0.7511 time to fit residues: 594.4587 Evaluate side-chains 636 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 584 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 339 GLN Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 339 GLN Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 339 GLN Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain N residue 120 GLU Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 393 ASN Chi-restraints excluded: chain Q residue 64 ASN Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 339 GLN Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 339 GLN Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain T residue 120 GLU Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 339 GLN Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain X residue 99 ASN Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 314 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 431 optimal weight: 7.9990 chunk 478 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 357 optimal weight: 4.9990 chunk 434 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 188 ASN A 359 ASN A 388 GLN B 96 ASN C 188 ASN C 262 ASN C 359 ASN C 388 GLN E 188 ASN E 388 GLN G 48 HIS G 188 ASN G 359 ASN G 388 GLN H 96 ASN I 188 ASN I 262 ASN I 359 ASN I 388 GLN K 188 ASN K 388 GLN M 48 HIS M 188 ASN M 359 ASN M 388 GLN N 96 ASN O 188 ASN O 262 ASN O 388 GLN Q 188 ASN Q 388 GLN S 48 HIS S 188 ASN S 388 GLN T 96 ASN U 188 ASN U 262 ASN U 359 ASN U 388 GLN W 188 ASN W 388 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.115548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.068059 restraints weight = 63009.268| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.41 r_work: 0.2553 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 41472 Z= 0.330 Angle : 0.610 5.654 55764 Z= 0.338 Chirality : 0.045 0.216 6300 Planarity : 0.004 0.042 7032 Dihedral : 4.279 22.226 5436 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.01 % Allowed : 9.93 % Favored : 87.06 % 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: 1.08 (0.12), residues: 4872 helix: 1.48 (0.10), residues: 2940 sheet: -0.36 (0.21), residues: 600 loop : -0.33 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 119 TYR 0.027 0.002 TYR K 73 PHE 0.024 0.002 PHE I 269 HIS 0.005 0.001 HIS I 121 Details of bonding type rmsd covalent geometry : bond 0.00808 (41472) covalent geometry : angle 0.60980 (55764) hydrogen bonds : bond 0.07374 ( 2388) hydrogen bonds : angle 4.78050 ( 6984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 556 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8913 (tptt) cc_final: 0.8484 (tppp) REVERT: A 110 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: A 157 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8325 (ptt90) REVERT: A 339 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8519 (mp10) REVERT: A 399 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8679 (tmm) REVERT: C 110 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: C 290 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: C 339 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8560 (mp-120) REVERT: C 399 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8831 (tmm) REVERT: E 86 LYS cc_start: 0.8608 (tptt) cc_final: 0.8167 (tppp) REVERT: E 110 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: E 399 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8672 (tmm) REVERT: F 114 MET cc_start: 0.7406 (mmp) cc_final: 0.7135 (tmm) REVERT: G 86 LYS cc_start: 0.8917 (tptt) cc_final: 0.8487 (tppp) REVERT: G 110 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: G 157 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8319 (ptt90) REVERT: G 339 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8518 (mp10) REVERT: G 399 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8674 (tmm) REVERT: I 110 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: I 290 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: I 339 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8559 (mp-120) REVERT: I 399 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8833 (tmm) REVERT: K 86 LYS cc_start: 0.8608 (tptt) cc_final: 0.8167 (tppp) REVERT: K 110 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: K 399 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8663 (tmm) REVERT: L 114 MET cc_start: 0.7410 (mmp) cc_final: 0.7136 (tmm) REVERT: M 86 LYS cc_start: 0.8915 (tptt) cc_final: 0.8487 (tppp) REVERT: M 110 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: M 157 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8313 (ptt90) REVERT: M 339 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8516 (mp10) REVERT: M 399 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8672 (tmm) REVERT: O 110 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: O 290 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: O 339 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8560 (mp-120) REVERT: O 399 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8817 (tmm) REVERT: Q 86 LYS cc_start: 0.8609 (tptt) cc_final: 0.8170 (tppp) REVERT: Q 110 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: Q 399 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8672 (tmm) REVERT: R 114 MET cc_start: 0.7416 (mmp) cc_final: 0.7141 (tmm) REVERT: S 86 LYS cc_start: 0.8914 (tptt) cc_final: 0.8486 (tppp) REVERT: S 110 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: S 157 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8321 (ptt90) REVERT: S 339 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: S 399 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8679 (tmm) REVERT: U 110 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: U 290 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: U 339 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8563 (mp-120) REVERT: U 399 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8819 (tmm) REVERT: W 86 LYS cc_start: 0.8605 (tptt) cc_final: 0.8160 (tppp) REVERT: W 110 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: W 399 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8671 (tmm) REVERT: X 114 MET cc_start: 0.7412 (mmp) cc_final: 0.7139 (tmm) outliers start: 136 outliers final: 40 residues processed: 620 average time/residue: 0.9264 time to fit residues: 676.4579 Evaluate side-chains 604 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 524 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 157 ARG Chi-restraints excluded: chain G residue 339 GLN Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 157 ARG Chi-restraints excluded: chain M residue 339 GLN Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 290 GLU Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 393 ASN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 159 ILE Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain Q residue 399 MET Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 110 GLU Chi-restraints excluded: chain S residue 157 ARG Chi-restraints excluded: chain S residue 339 GLN Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 140 ILE Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 290 GLU Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain V residue 159 ILE Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain W residue 399 MET Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 166 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 290 optimal weight: 0.5980 chunk 214 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 440 optimal weight: 0.6980 chunk 318 optimal weight: 9.9990 chunk 475 optimal weight: 20.0000 chunk 246 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 262 ASN A 385 GLN A 388 GLN C 320 ASN C 388 GLN E 359 ASN E 388 GLN F 96 ASN G 121 HIS G 262 ASN G 385 GLN G 388 GLN I 320 ASN I 388 GLN K 314 GLN K 359 ASN K 388 GLN L 96 ASN M 121 HIS M 262 ASN M 385 GLN M 388 GLN O 320 ASN O 359 ASN O 388 GLN Q 314 GLN Q 359 ASN Q 388 GLN R 96 ASN S 121 HIS S 262 ASN S 359 ASN S 385 GLN S 388 GLN U 320 ASN U 388 GLN W 314 GLN W 359 ASN W 388 GLN X 96 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.074485 restraints weight = 62700.012| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.44 r_work: 0.2685 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 41472 Z= 0.103 Angle : 0.458 7.103 55764 Z= 0.253 Chirality : 0.038 0.178 6300 Planarity : 0.003 0.035 7032 Dihedral : 3.921 17.997 5436 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.86 % Allowed : 11.44 % Favored : 86.70 % 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: 1.70 (0.12), residues: 4872 helix: 1.93 (0.10), residues: 2952 sheet: -0.02 (0.21), residues: 576 loop : -0.04 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 326 TYR 0.016 0.001 TYR Q 177 PHE 0.014 0.001 PHE W 269 HIS 0.003 0.001 HIS U 121 Details of bonding type rmsd covalent geometry : bond 0.00218 (41472) covalent geometry : angle 0.45832 (55764) hydrogen bonds : bond 0.04166 ( 2388) hydrogen bonds : angle 4.28490 ( 6984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 539 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8941 (tptt) cc_final: 0.8537 (tppp) REVERT: A 149 GLU cc_start: 0.8922 (pt0) cc_final: 0.8699 (pt0) REVERT: A 399 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8650 (tmm) REVERT: C 339 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8587 (mp-120) REVERT: C 399 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8812 (tmm) REVERT: E 86 LYS cc_start: 0.8569 (tptt) cc_final: 0.8199 (tppp) REVERT: E 113 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.8066 (tpp-160) REVERT: E 157 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8231 (ptt180) REVERT: E 399 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8625 (tmm) REVERT: G 86 LYS cc_start: 0.8943 (tptt) cc_final: 0.8540 (tppp) REVERT: G 399 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8657 (tmm) REVERT: I 339 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8592 (mp-120) REVERT: I 399 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8811 (tmm) REVERT: K 86 LYS cc_start: 0.8555 (tptt) cc_final: 0.8188 (tppp) REVERT: K 113 ARG cc_start: 0.8298 (tpp-160) cc_final: 0.8074 (tpp-160) REVERT: K 157 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8229 (ptt180) REVERT: K 313 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8724 (mm-30) REVERT: K 399 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8621 (tmm) REVERT: M 86 LYS cc_start: 0.8939 (tptt) cc_final: 0.8535 (tppp) REVERT: M 399 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8661 (tmm) REVERT: O 339 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8589 (mp-120) REVERT: O 399 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8802 (tmm) REVERT: Q 86 LYS cc_start: 0.8563 (tptt) cc_final: 0.8197 (tppp) REVERT: Q 113 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.8091 (tpp-160) REVERT: Q 157 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8240 (ptt180) REVERT: Q 313 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8723 (mm-30) REVERT: Q 399 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8623 (tmm) REVERT: S 86 LYS cc_start: 0.8939 (tptt) cc_final: 0.8536 (tppp) REVERT: S 149 GLU cc_start: 0.8909 (pt0) cc_final: 0.8686 (pt0) REVERT: S 399 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8656 (tmm) REVERT: U 339 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8588 (mp-120) REVERT: U 399 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8806 (tmm) REVERT: W 86 LYS cc_start: 0.8562 (tptt) cc_final: 0.8162 (tppp) REVERT: W 113 ARG cc_start: 0.8306 (tpp-160) cc_final: 0.8084 (tpp-160) REVERT: W 157 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8240 (ptt180) REVERT: W 313 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8729 (mm-30) REVERT: W 399 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8622 (tmm) outliers start: 84 outliers final: 12 residues processed: 571 average time/residue: 0.8942 time to fit residues: 604.8021 Evaluate side-chains 555 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 523 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain Q residue 64 ASN Chi-restraints excluded: chain Q residue 157 ARG Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain Q residue 399 MET Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 157 ARG Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain W residue 399 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 42 optimal weight: 0.9990 chunk 410 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 437 optimal weight: 0.9990 chunk 327 optimal weight: 6.9990 chunk 462 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 415 optimal weight: 0.8980 chunk 446 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 380 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 385 GLN A 388 GLN C 188 ASN C 388 GLN E 188 ASN E 388 GLN F 96 ASN G 385 GLN G 388 GLN I 388 GLN K 388 GLN L 96 ASN M 188 ASN M 385 GLN M 388 GLN O 188 ASN O 388 GLN Q 388 GLN R 96 ASN S 188 ASN S 385 GLN S 388 GLN U 188 ASN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.074729 restraints weight = 62816.378| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.43 r_work: 0.2692 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41472 Z= 0.099 Angle : 0.451 7.003 55764 Z= 0.246 Chirality : 0.038 0.158 6300 Planarity : 0.003 0.027 7032 Dihedral : 3.788 18.829 5436 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.51 % Allowed : 12.26 % Favored : 86.24 % 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: 1.76 (0.12), residues: 4872 helix: 2.06 (0.10), residues: 2940 sheet: 0.13 (0.21), residues: 576 loop : -0.31 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 326 TYR 0.017 0.001 TYR W 177 PHE 0.013 0.001 PHE Q 269 HIS 0.005 0.001 HIS I 121 Details of bonding type rmsd covalent geometry : bond 0.00209 (41472) covalent geometry : angle 0.45064 (55764) hydrogen bonds : bond 0.04068 ( 2388) hydrogen bonds : angle 4.19715 ( 6984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 528 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8926 (m-40) REVERT: A 86 LYS cc_start: 0.8957 (tptt) cc_final: 0.8550 (tppp) REVERT: A 313 GLU cc_start: 0.8939 (tp30) cc_final: 0.8735 (mm-30) REVERT: A 399 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8658 (tmm) REVERT: C 339 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8619 (mp-120) REVERT: C 399 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8828 (tmm) REVERT: D 156 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8080 (mptt) REVERT: E 86 LYS cc_start: 0.8632 (tptt) cc_final: 0.8246 (tppp) REVERT: E 157 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8155 (ptt180) REVERT: E 313 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8702 (mm-30) REVERT: E 339 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8703 (mp10) REVERT: E 399 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8675 (tmm) REVERT: G 64 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8930 (m-40) REVERT: G 86 LYS cc_start: 0.8958 (tptt) cc_final: 0.8551 (tppp) REVERT: G 313 GLU cc_start: 0.8933 (tp30) cc_final: 0.8732 (mm-30) REVERT: G 399 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8668 (tmm) REVERT: I 339 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8613 (mp-120) REVERT: I 399 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8814 (tmm) REVERT: J 156 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8083 (mptt) REVERT: K 86 LYS cc_start: 0.8622 (tptt) cc_final: 0.8235 (tppp) REVERT: K 157 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8146 (ptt180) REVERT: K 313 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8708 (mm-30) REVERT: K 339 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: K 399 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8667 (tmm) REVERT: L 114 MET cc_start: 0.7327 (mmp) cc_final: 0.7117 (tmm) REVERT: M 64 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8928 (m-40) REVERT: M 86 LYS cc_start: 0.8962 (tptt) cc_final: 0.8552 (tppp) REVERT: M 313 GLU cc_start: 0.8944 (tp30) cc_final: 0.8741 (mm-30) REVERT: M 399 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8670 (tmm) REVERT: O 339 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8613 (mp-120) REVERT: O 399 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8811 (tmm) REVERT: P 156 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8078 (mptt) REVERT: Q 86 LYS cc_start: 0.8626 (tptt) cc_final: 0.8239 (tppp) REVERT: Q 157 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8167 (ptt180) REVERT: Q 313 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8710 (mm-30) REVERT: Q 339 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8698 (mp10) REVERT: Q 399 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8656 (tmm) REVERT: R 114 MET cc_start: 0.7327 (mmp) cc_final: 0.7115 (tmm) REVERT: S 64 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8927 (m-40) REVERT: S 86 LYS cc_start: 0.8953 (tptt) cc_final: 0.8544 (tppp) REVERT: S 313 GLU cc_start: 0.8937 (tp30) cc_final: 0.8732 (mm-30) REVERT: S 399 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8668 (tmm) REVERT: U 339 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8612 (mp-120) REVERT: U 399 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8809 (tmm) REVERT: V 156 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8085 (mptt) REVERT: W 86 LYS cc_start: 0.8615 (tptt) cc_final: 0.8234 (tppp) REVERT: W 157 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8162 (ptt180) REVERT: W 313 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8711 (mm-30) REVERT: W 339 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8702 (mp10) REVERT: W 399 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8673 (tmm) REVERT: X 114 MET cc_start: 0.7299 (mmp) cc_final: 0.7098 (tmm) outliers start: 68 outliers final: 12 residues processed: 556 average time/residue: 0.9033 time to fit residues: 593.9698 Evaluate side-chains 551 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 511 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 339 GLN Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 339 GLN Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain Q residue 157 ARG Chi-restraints excluded: chain Q residue 339 GLN Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain Q residue 399 MET Chi-restraints excluded: chain S residue 64 ASN Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain W residue 157 ARG Chi-restraints excluded: chain W residue 339 GLN Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain W residue 399 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 220 optimal weight: 3.9990 chunk 439 optimal weight: 9.9990 chunk 330 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 325 optimal weight: 0.9980 chunk 448 optimal weight: 8.9990 chunk 359 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 388 GLN B 158 ASN C 262 ASN C 388 GLN E 388 GLN F 96 ASN G 385 GLN G 388 GLN H 158 ASN I 262 ASN I 388 GLN K 388 GLN L 96 ASN M 385 GLN M 388 GLN N 158 ASN O 262 ASN O 388 GLN Q 388 GLN R 96 ASN S 385 GLN S 388 GLN T 158 ASN U 262 ASN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.072312 restraints weight = 62909.865| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.38 r_work: 0.2635 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41472 Z= 0.139 Angle : 0.481 7.015 55764 Z= 0.266 Chirality : 0.040 0.160 6300 Planarity : 0.003 0.024 7032 Dihedral : 3.891 19.496 5436 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.04 % Allowed : 12.63 % Favored : 85.33 % 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: 1.65 (0.12), residues: 4872 helix: 2.02 (0.10), residues: 2928 sheet: -0.04 (0.21), residues: 576 loop : -0.38 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 326 TYR 0.021 0.001 TYR S 177 PHE 0.016 0.001 PHE C 269 HIS 0.006 0.001 HIS I 121 Details of bonding type rmsd covalent geometry : bond 0.00321 (41472) covalent geometry : angle 0.48113 (55764) hydrogen bonds : bond 0.04956 ( 2388) hydrogen bonds : angle 4.24843 ( 6984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 522 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8969 (tptt) cc_final: 0.8546 (tppp) REVERT: A 399 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8649 (tmm) REVERT: C 339 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8554 (mp-120) REVERT: C 399 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8833 (tmm) REVERT: E 86 LYS cc_start: 0.8619 (tptt) cc_final: 0.8215 (tppp) REVERT: E 157 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8234 (ptt180) REVERT: E 399 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8685 (tmm) REVERT: G 86 LYS cc_start: 0.8975 (tptt) cc_final: 0.8552 (tppp) REVERT: G 399 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8656 (tmm) REVERT: I 339 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8550 (mp-120) REVERT: I 399 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8846 (tmm) REVERT: K 86 LYS cc_start: 0.8605 (tptt) cc_final: 0.8146 (tppp) REVERT: K 157 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8239 (ptt180) REVERT: K 399 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8672 (tmm) REVERT: L 114 MET cc_start: 0.7450 (mmp) cc_final: 0.7198 (tmm) REVERT: M 86 LYS cc_start: 0.8973 (tptt) cc_final: 0.8548 (tppp) REVERT: M 399 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8661 (tmm) REVERT: O 339 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8561 (mp-120) REVERT: O 399 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8837 (tmm) REVERT: Q 86 LYS cc_start: 0.8612 (tptt) cc_final: 0.8152 (tppp) REVERT: Q 157 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8240 (ptt180) REVERT: Q 399 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (tmm) REVERT: R 114 MET cc_start: 0.7449 (mmp) cc_final: 0.7199 (tmm) REVERT: S 86 LYS cc_start: 0.8969 (tptt) cc_final: 0.8547 (tppp) REVERT: S 399 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8655 (tmm) REVERT: U 339 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8563 (mp-120) REVERT: U 399 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8835 (tmm) REVERT: W 86 LYS cc_start: 0.8606 (tptt) cc_final: 0.8207 (tppp) REVERT: W 157 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8248 (ptt180) REVERT: W 399 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8675 (tmm) REVERT: X 114 MET cc_start: 0.7444 (mmp) cc_final: 0.7167 (tmm) outliers start: 92 outliers final: 28 residues processed: 562 average time/residue: 0.8718 time to fit residues: 582.5986 Evaluate side-chains 552 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 504 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain Q residue 157 ARG Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain Q residue 399 MET Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain W residue 157 ARG Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain W residue 399 MET Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 475 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 443 optimal weight: 7.9990 chunk 449 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 430 optimal weight: 3.9990 chunk 467 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 385 GLN A 388 GLN B 158 ASN C 262 ASN C 388 GLN E 388 GLN F 96 ASN G 385 GLN G 388 GLN H 158 ASN I 262 ASN I 388 GLN K 388 GLN L 96 ASN M 385 GLN M 388 GLN N 158 ASN O 262 ASN O 388 GLN Q 388 GLN R 96 ASN S 121 HIS S 385 GLN S 388 GLN T 158 ASN U 262 ASN U 388 GLN ** U 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 388 GLN X 96 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.072912 restraints weight = 62770.629| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.41 r_work: 0.2651 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41472 Z= 0.121 Angle : 0.478 9.942 55764 Z= 0.263 Chirality : 0.039 0.163 6300 Planarity : 0.003 0.035 7032 Dihedral : 3.862 19.723 5436 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.68 % Allowed : 13.05 % Favored : 85.26 % 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: 1.66 (0.12), residues: 4872 helix: 2.04 (0.10), residues: 2928 sheet: -0.05 (0.21), residues: 576 loop : -0.39 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 326 TYR 0.020 0.001 TYR W 177 PHE 0.014 0.001 PHE O 269 HIS 0.005 0.001 HIS I 121 Details of bonding type rmsd covalent geometry : bond 0.00273 (41472) covalent geometry : angle 0.47826 (55764) hydrogen bonds : bond 0.04542 ( 2388) hydrogen bonds : angle 4.22108 ( 6984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 522 time to evaluate : 1.738 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: A 64 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8971 (m-40) REVERT: A 86 LYS cc_start: 0.8954 (tptt) cc_final: 0.8538 (tppp) REVERT: A 399 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8744 (tmm) REVERT: B 123 ARG cc_start: 0.7136 (mtt90) cc_final: 0.6918 (mtt90) REVERT: C 119 PHE cc_start: 0.8563 (m-80) cc_final: 0.8249 (m-80) REVERT: C 339 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8435 (mp-120) REVERT: C 399 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8850 (tmm) REVERT: E 86 LYS cc_start: 0.8645 (tptt) cc_final: 0.8202 (tppp) REVERT: E 157 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8234 (ptt180) REVERT: E 399 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8666 (tmm) REVERT: G 64 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8968 (m-40) REVERT: G 86 LYS cc_start: 0.8960 (tptt) cc_final: 0.8543 (tppp) REVERT: G 399 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8745 (tmm) REVERT: H 123 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6914 (mtt90) REVERT: I 119 PHE cc_start: 0.8557 (m-80) cc_final: 0.8241 (m-80) REVERT: I 339 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8433 (mp-120) REVERT: I 399 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8854 (tmm) REVERT: K 86 LYS cc_start: 0.8619 (tptt) cc_final: 0.8171 (tppp) REVERT: K 157 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8234 (ptt180) REVERT: K 399 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8655 (tmm) REVERT: L 114 MET cc_start: 0.7462 (mmp) cc_final: 0.7188 (tmm) REVERT: M 64 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8966 (m-40) REVERT: M 86 LYS cc_start: 0.8960 (tptt) cc_final: 0.8539 (tppp) REVERT: M 399 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8739 (tmm) REVERT: N 123 ARG cc_start: 0.7124 (mtt90) cc_final: 0.6906 (mtt90) REVERT: O 119 PHE cc_start: 0.8558 (m-80) cc_final: 0.8242 (m-80) REVERT: O 339 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8440 (mp-120) REVERT: O 399 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8855 (tmm) REVERT: Q 86 LYS cc_start: 0.8625 (tptt) cc_final: 0.8176 (tppp) REVERT: Q 157 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8241 (ptt180) REVERT: Q 399 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8654 (tmm) REVERT: R 114 MET cc_start: 0.7461 (mmp) cc_final: 0.7190 (tmm) REVERT: S 64 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8969 (m-40) REVERT: S 86 LYS cc_start: 0.8956 (tptt) cc_final: 0.8536 (tppp) REVERT: S 399 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8739 (tmm) REVERT: T 123 ARG cc_start: 0.7118 (mtt90) cc_final: 0.6899 (mtt90) REVERT: U 119 PHE cc_start: 0.8558 (m-80) cc_final: 0.8245 (m-80) REVERT: U 339 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8440 (mp-120) REVERT: U 399 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8852 (tmm) REVERT: W 86 LYS cc_start: 0.8613 (tptt) cc_final: 0.8161 (tppp) REVERT: W 157 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8248 (ptt180) REVERT: W 399 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8658 (tmm) outliers start: 76 outliers final: 40 residues processed: 554 average time/residue: 0.8673 time to fit residues: 572.0234 Evaluate side-chains 575 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 511 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 157 ARG Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain Q residue 399 MET Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 64 ASN Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 157 ARG Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain W residue 399 MET Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 474 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 468 optimal weight: 3.9990 chunk 457 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 385 GLN A 388 GLN C 262 ASN C 388 GLN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 GLN G 388 GLN I 262 ASN I 388 GLN ** I 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 388 GLN L 96 ASN ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 385 GLN M 388 GLN O 188 ASN O 262 ASN O 388 GLN ** O 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 388 GLN R 96 ASN S 121 HIS S 385 GLN S 388 GLN U 262 ASN U 388 GLN ** U 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 388 GLN X 96 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.070966 restraints weight = 62619.191| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.40 r_work: 0.2612 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41472 Z= 0.164 Angle : 0.502 9.643 55764 Z= 0.278 Chirality : 0.040 0.179 6300 Planarity : 0.003 0.039 7032 Dihedral : 3.972 20.773 5436 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.97 % Allowed : 13.48 % Favored : 84.55 % 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: 1.54 (0.12), residues: 4872 helix: 1.93 (0.10), residues: 2928 sheet: -0.03 (0.21), residues: 576 loop : -0.45 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 326 TYR 0.022 0.001 TYR A 177 PHE 0.017 0.001 PHE I 269 HIS 0.006 0.001 HIS O 121 Details of bonding type rmsd covalent geometry : bond 0.00389 (41472) covalent geometry : angle 0.50205 (55764) hydrogen bonds : bond 0.05321 ( 2388) hydrogen bonds : angle 4.32149 ( 6984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 509 time to evaluate : 1.758 Fit side-chains revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8954 (tptt) cc_final: 0.8491 (tppp) REVERT: A 399 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8743 (tmm) REVERT: C 339 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8388 (mp-120) REVERT: C 399 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8842 (tmm) REVERT: E 86 LYS cc_start: 0.8619 (tptt) cc_final: 0.8165 (tppp) REVERT: E 157 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8234 (ptt180) REVERT: E 399 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8664 (tmm) REVERT: G 86 LYS cc_start: 0.8960 (tptt) cc_final: 0.8500 (tppp) REVERT: G 399 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8738 (tmm) REVERT: I 339 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8387 (mp-120) REVERT: I 399 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8844 (tmm) REVERT: K 86 LYS cc_start: 0.8606 (tptt) cc_final: 0.8214 (tppp) REVERT: K 157 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8248 (ptt180) REVERT: K 399 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8663 (tmm) REVERT: M 86 LYS cc_start: 0.8964 (tptt) cc_final: 0.8499 (tppp) REVERT: M 399 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8752 (tmm) REVERT: O 339 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8395 (mp-120) REVERT: O 399 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8826 (tmm) REVERT: Q 86 LYS cc_start: 0.8611 (tptt) cc_final: 0.8222 (tppp) REVERT: Q 157 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8246 (ptt180) REVERT: Q 399 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8660 (tmm) REVERT: S 86 LYS cc_start: 0.8956 (tptt) cc_final: 0.8493 (tppp) REVERT: S 399 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8744 (tmm) REVERT: U 339 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8396 (mp-120) REVERT: U 399 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8829 (tmm) REVERT: W 86 LYS cc_start: 0.8611 (tptt) cc_final: 0.8148 (tppp) REVERT: W 157 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8251 (ptt180) REVERT: W 399 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8667 (tmm) outliers start: 89 outliers final: 48 residues processed: 549 average time/residue: 0.8791 time to fit residues: 575.5973 Evaluate side-chains 561 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 493 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 157 ARG Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain Q residue 399 MET Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 157 ARG Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain W residue 399 MET Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 15 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 388 optimal weight: 0.8980 chunk 377 optimal weight: 6.9990 chunk 419 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 431 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 chunk 230 optimal weight: 0.3980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 385 GLN A 388 GLN C 388 GLN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS E 388 GLN F 96 ASN G 121 HIS G 385 GLN G 388 GLN I 262 ASN I 388 GLN ** I 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 HIS K 388 GLN L 96 ASN M 121 HIS M 385 GLN M 388 GLN O 262 ASN O 388 GLN ** O 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 HIS Q 388 GLN R 96 ASN S 121 HIS S 385 GLN S 388 GLN U 262 ASN U 388 GLN ** U 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 HIS W 388 GLN X 96 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.071795 restraints weight = 62866.875| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.43 r_work: 0.2630 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41472 Z= 0.136 Angle : 0.496 9.266 55764 Z= 0.272 Chirality : 0.040 0.205 6300 Planarity : 0.003 0.042 7032 Dihedral : 3.934 20.770 5436 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.62 % Allowed : 13.70 % Favored : 84.69 % 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: 1.62 (0.12), residues: 4872 helix: 2.00 (0.10), residues: 2928 sheet: 0.04 (0.21), residues: 576 loop : -0.46 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 326 TYR 0.021 0.001 TYR C 177 PHE 0.015 0.001 PHE C 269 HIS 0.006 0.001 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00316 (41472) covalent geometry : angle 0.49610 (55764) hydrogen bonds : bond 0.04847 ( 2388) hydrogen bonds : angle 4.29737 ( 6984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 500 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8950 (tptt) cc_final: 0.8501 (tppp) REVERT: C 110 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: C 119 PHE cc_start: 0.8538 (m-80) cc_final: 0.8234 (m-80) REVERT: C 339 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8388 (mp-120) REVERT: C 399 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8848 (tmm) REVERT: E 86 LYS cc_start: 0.8628 (tptt) cc_final: 0.8184 (tppp) REVERT: E 157 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8234 (ptt180) REVERT: E 399 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8673 (tmm) REVERT: F 156 LYS cc_start: 0.8090 (mppt) cc_final: 0.7762 (mtmt) REVERT: G 86 LYS cc_start: 0.8952 (tptt) cc_final: 0.8504 (tppp) REVERT: I 110 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: I 119 PHE cc_start: 0.8534 (m-80) cc_final: 0.8228 (m-80) REVERT: I 339 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8389 (mp-120) REVERT: I 399 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8838 (tmm) REVERT: K 86 LYS cc_start: 0.8598 (tptt) cc_final: 0.8210 (tppp) REVERT: K 157 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8237 (ptt180) REVERT: K 399 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8676 (tmm) REVERT: L 156 LYS cc_start: 0.8068 (mppt) cc_final: 0.7749 (mtmt) REVERT: M 86 LYS cc_start: 0.8955 (tptt) cc_final: 0.8503 (tppp) REVERT: O 110 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: O 119 PHE cc_start: 0.8537 (m-80) cc_final: 0.8231 (m-80) REVERT: O 339 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8393 (mp-120) REVERT: O 399 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8832 (tmm) REVERT: Q 86 LYS cc_start: 0.8604 (tptt) cc_final: 0.8217 (tppp) REVERT: Q 157 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8244 (ptt180) REVERT: Q 399 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8674 (tmm) REVERT: R 156 LYS cc_start: 0.8062 (mppt) cc_final: 0.7747 (mtmt) REVERT: S 86 LYS cc_start: 0.8949 (tptt) cc_final: 0.8498 (tppp) REVERT: U 110 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: U 119 PHE cc_start: 0.8525 (m-80) cc_final: 0.8218 (m-80) REVERT: U 339 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8397 (mp-120) REVERT: U 399 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8831 (tmm) REVERT: W 86 LYS cc_start: 0.8604 (tptt) cc_final: 0.8218 (tppp) REVERT: W 157 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8245 (ptt180) REVERT: W 399 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8675 (tmm) REVERT: X 156 LYS cc_start: 0.8090 (mppt) cc_final: 0.7781 (mtmt) outliers start: 73 outliers final: 47 residues processed: 528 average time/residue: 0.8969 time to fit residues: 561.6696 Evaluate side-chains 559 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 492 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 157 ARG Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain Q residue 399 MET Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 157 ARG Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain W residue 399 MET Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 358 optimal weight: 5.9990 chunk 473 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 50 optimal weight: 0.0770 chunk 4 optimal weight: 5.9990 chunk 444 optimal weight: 3.9990 chunk 392 optimal weight: 7.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 385 GLN A 388 GLN C 388 GLN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 GLN G 388 GLN I 388 GLN ** I 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 HIS K 388 GLN L 96 ASN ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 385 GLN M 388 GLN O 388 GLN ** O 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 HIS Q 388 GLN R 96 ASN S 121 HIS S 385 GLN S 388 GLN U 388 GLN ** U 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 HIS W 388 GLN X 96 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.071409 restraints weight = 62476.610| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.38 r_work: 0.2618 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41472 Z= 0.149 Angle : 0.491 7.400 55764 Z= 0.273 Chirality : 0.040 0.204 6300 Planarity : 0.003 0.044 7032 Dihedral : 3.966 21.516 5436 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.66 % Allowed : 13.59 % Favored : 84.75 % 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: 1.57 (0.12), residues: 4872 helix: 1.96 (0.10), residues: 2928 sheet: 0.04 (0.21), residues: 576 loop : -0.48 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 326 TYR 0.021 0.001 TYR C 177 PHE 0.016 0.001 PHE O 269 HIS 0.007 0.001 HIS I 121 Details of bonding type rmsd covalent geometry : bond 0.00349 (41472) covalent geometry : angle 0.49129 (55764) hydrogen bonds : bond 0.05107 ( 2388) hydrogen bonds : angle 4.30653 ( 6984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 505 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8951 (tptt) cc_final: 0.8483 (tppp) REVERT: C 48 HIS cc_start: 0.8154 (m-70) cc_final: 0.7877 (m90) REVERT: C 110 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: C 119 PHE cc_start: 0.8517 (m-80) cc_final: 0.8208 (m-80) REVERT: C 339 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8374 (mp-120) REVERT: C 399 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8834 (tmm) REVERT: E 86 LYS cc_start: 0.8629 (tptt) cc_final: 0.8252 (tppp) REVERT: E 157 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8236 (ptt180) REVERT: E 399 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8653 (tmm) REVERT: F 156 LYS cc_start: 0.8089 (mppt) cc_final: 0.7792 (mtmt) REVERT: G 86 LYS cc_start: 0.8953 (tptt) cc_final: 0.8488 (tppp) REVERT: I 48 HIS cc_start: 0.8157 (m-70) cc_final: 0.7881 (m90) REVERT: I 110 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: I 119 PHE cc_start: 0.8518 (m-80) cc_final: 0.8205 (m-80) REVERT: I 339 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8374 (mp-120) REVERT: I 399 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8827 (tmm) REVERT: K 86 LYS cc_start: 0.8604 (tptt) cc_final: 0.8213 (tppp) REVERT: K 157 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8245 (ptt180) REVERT: K 399 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8665 (tmm) REVERT: L 156 LYS cc_start: 0.8059 (mppt) cc_final: 0.7771 (mtmt) REVERT: M 86 LYS cc_start: 0.8957 (tptt) cc_final: 0.8487 (tppp) REVERT: O 48 HIS cc_start: 0.8149 (m-70) cc_final: 0.7872 (m90) REVERT: O 110 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: O 119 PHE cc_start: 0.8510 (m-80) cc_final: 0.8199 (m-80) REVERT: O 339 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8369 (mp-120) REVERT: O 399 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8817 (tmm) REVERT: Q 86 LYS cc_start: 0.8602 (tptt) cc_final: 0.8214 (tppp) REVERT: Q 157 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8248 (ptt180) REVERT: Q 399 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8661 (tmm) REVERT: R 156 LYS cc_start: 0.8057 (mppt) cc_final: 0.7771 (mtmt) REVERT: S 86 LYS cc_start: 0.8957 (tptt) cc_final: 0.8487 (tppp) REVERT: U 48 HIS cc_start: 0.8146 (m-70) cc_final: 0.7869 (m90) REVERT: U 110 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: U 119 PHE cc_start: 0.8512 (m-80) cc_final: 0.8201 (m-80) REVERT: U 339 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8381 (mp-120) REVERT: U 399 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8820 (tmm) REVERT: W 86 LYS cc_start: 0.8604 (tptt) cc_final: 0.8212 (tppp) REVERT: W 157 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8244 (ptt180) REVERT: W 399 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8657 (tmm) REVERT: X 156 LYS cc_start: 0.8094 (mppt) cc_final: 0.7818 (mtmt) outliers start: 75 outliers final: 51 residues processed: 540 average time/residue: 0.8777 time to fit residues: 563.6737 Evaluate side-chains 559 residues out of total 4512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 488 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ARG Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 157 ARG Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain Q residue 399 MET Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 157 ARG Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain W residue 399 MET Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 68 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 452 optimal weight: 9.9990 chunk 349 optimal weight: 5.9990 chunk 115 optimal weight: 0.2980 chunk 141 optimal weight: 0.7980 chunk 348 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 437 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 385 GLN A 388 GLN C 388 GLN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS E 388 GLN F 96 ASN G 121 HIS G 385 GLN G 388 GLN I 388 GLN ** I 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 HIS K 388 GLN L 96 ASN M 121 HIS M 385 GLN M 388 GLN O 388 GLN ** O 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 HIS Q 388 GLN R 96 ASN S 121 HIS S 385 GLN S 388 GLN U 388 GLN ** U 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 HIS W 388 GLN X 96 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.072784 restraints weight = 62874.593| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.43 r_work: 0.2653 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41472 Z= 0.114 Angle : 0.477 9.791 55764 Z= 0.261 Chirality : 0.039 0.211 6300 Planarity : 0.003 0.044 7032 Dihedral : 3.875 21.173 5436 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.51 % Allowed : 13.96 % Favored : 84.53 % 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: 1.73 (0.12), residues: 4872 helix: 2.10 (0.10), residues: 2928 sheet: 0.07 (0.21), residues: 576 loop : -0.43 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 326 TYR 0.019 0.001 TYR K 177 PHE 0.013 0.001 PHE E 269 HIS 0.007 0.001 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00254 (41472) covalent geometry : angle 0.47689 (55764) hydrogen bonds : bond 0.04422 ( 2388) hydrogen bonds : angle 4.21312 ( 6984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21014.81 seconds wall clock time: 357 minutes 48.77 seconds (21468.77 seconds total)