Starting phenix.real_space_refine on Sun Aug 24 10:13:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eeu_28058/08_2025/8eeu_28058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eeu_28058/08_2025/8eeu_28058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eeu_28058/08_2025/8eeu_28058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eeu_28058/08_2025/8eeu_28058.map" model { file = "/net/cci-nas-00/data/ceres_data/8eeu_28058/08_2025/8eeu_28058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eeu_28058/08_2025/8eeu_28058.cif" } resolution = 3.5 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= 0.002 sd= 0.031 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 124 5.16 5 C 12093 2.51 5 N 3265 2.21 5 O 3645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s 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: 19127 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3067 Classifications: {'peptide': 402} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain: "B" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2685 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 23, 'TRANS': 317} Chain breaks: 1 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2969 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 359} Chain breaks: 2 Chain: "D" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2794 Classifications: {'peptide': 354} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 327} Chain breaks: 1 Chain: "E" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3025 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 367} Chain: "F" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2799 Classifications: {'peptide': 355} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 327} Chain breaks: 1 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 975 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Time building chain proxies: 4.16, per 1000 atoms: 0.22 Number of scatterers: 19127 At special positions: 0 Unit cell: (160.512, 143.616, 149.952, 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 124 16.00 O 3645 8.00 N 3265 7.00 C 12093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.02 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.04 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.02 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 104 " distance=2.02 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.04 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 27 " distance=2.03 Simple disulfide: pdb=" SG CYS D 90 " - pdb=" SG CYS D 104 " distance=2.02 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.04 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.02 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 78 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.04 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.02 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 27 " distance=2.02 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 104 " distance=2.02 Simple disulfide: pdb=" SG CYS F 151 " - pdb=" SG CYS F 266 " distance=2.03 Simple disulfide: pdb=" SG CYS F 200 " - pdb=" SG CYS F 226 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 1.07 Conformation dependent library (CDL) restraints added in 626.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 70 sheets defined 3.0% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.518A pdb=" N GLN C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 removed outlier: 4.087A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.765A pdb=" N TYR D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 116 removed outlier: 4.511A pdb=" N LEU E 115 " --> pdb=" O ASP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.643A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 5.402A pdb=" N ILE A 31 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 134 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 35 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A 128 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 48 removed outlier: 7.006A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.591A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 281 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AB1, first strand: chain 'A' and resid 338 through 339 removed outlier: 6.390A pdb=" N THR A 317 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU A 303 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS A 319 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N CYS A 301 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 301 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS A 377 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 303 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.136A pdb=" N ARG B 103 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 92 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 52 through 55 removed outlier: 6.471A pdb=" N THR B 65 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AB8, first strand: chain 'B' and resid 147 through 154 Processing sheet with id=AB9, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AC1, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.776A pdb=" N SER B 195 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS B 206 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AC3, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AC4, first strand: chain 'C' and resid 3 through 8 removed outlier: 4.019A pdb=" N THR C 5 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AC6, first strand: chain 'C' and resid 35 through 48 removed outlier: 4.015A pdb=" N LYS C 35 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR C 126 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASN C 43 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 45 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 47 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 35 through 48 removed outlier: 4.015A pdb=" N LYS C 35 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR C 126 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASN C 43 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 45 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 47 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.659A pdb=" N ALA C 59 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD1, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.699A pdb=" N VAL C 154 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AD4, first strand: chain 'C' and resid 260 through 262 Processing sheet with id=AD5, first strand: chain 'C' and resid 302 through 306 removed outlier: 6.367A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 364 through 368 Processing sheet with id=AD7, first strand: chain 'D' and resid 17 through 19 removed outlier: 3.902A pdb=" N CYS D 19 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS D 27 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 33 through 37 removed outlier: 7.705A pdb=" N ILE D 33 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 50 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N SER D 50 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP D 69 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR D 65 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 68 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 33 through 37 removed outlier: 7.705A pdb=" N ILE D 33 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 50 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR D 98 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N SER D 51 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS D 96 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N TYR D 53 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N ASP D 94 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 15.009A pdb=" N LEU D 55 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 16.913A pdb=" N ILE D 92 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 83 through 85 Processing sheet with id=AE2, first strand: chain 'D' and resid 147 through 154 Processing sheet with id=AE3, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AE4, first strand: chain 'D' and resid 173 through 175 removed outlier: 3.652A pdb=" N GLU D 173 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 228 " --> pdb=" O ASP D 175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 179 through 180 Processing sheet with id=AE6, first strand: chain 'D' and resid 275 through 279 removed outlier: 3.643A pdb=" N VAL D 283 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 315 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 307 through 311 Processing sheet with id=AE8, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.785A pdb=" N THR E 5 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 278 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.480A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN E 134 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 35 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 39 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL E 47 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.480A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN E 134 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 35 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 39 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL E 47 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 51 through 55 Processing sheet with id=AF3, first strand: chain 'E' and resid 51 through 55 Processing sheet with id=AF4, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AF5, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AF6, first strand: chain 'E' and resid 260 through 262 removed outlier: 3.928A pdb=" N ARG E 267 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 300 through 306 removed outlier: 6.661A pdb=" N ILE E 315 " --> pdb=" O ASN E 304 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 326 through 328 Processing sheet with id=AF9, first strand: chain 'E' and resid 364 through 368 Processing sheet with id=AG1, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AG2, first strand: chain 'F' and resid 33 through 37 removed outlier: 8.402A pdb=" N ILE F 33 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 50 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 35 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N SER F 50 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP F 69 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR F 68 " --> pdb=" O LYS F 75 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 33 through 37 removed outlier: 8.402A pdb=" N ILE F 33 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 50 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 35 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR F 98 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N SER F 51 " --> pdb=" O HIS F 96 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS F 96 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N TYR F 53 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N ASP F 94 " --> pdb=" O TYR F 53 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 83 through 85 removed outlier: 3.696A pdb=" N SER F 109 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR F 127 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR F 111 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL F 125 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU F 113 " --> pdb=" O CYS F 123 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS F 123 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS F 115 " --> pdb=" O HIS F 121 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS F 121 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 147 through 154 Processing sheet with id=AG6, first strand: chain 'F' and resid 237 through 238 Processing sheet with id=AG7, first strand: chain 'F' and resid 173 through 174 removed outlier: 3.503A pdb=" N GLU F 173 " --> pdb=" O ARG F 230 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 179 through 181 Processing sheet with id=AG9, first strand: chain 'F' and resid 275 through 279 Processing sheet with id=AH1, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AH2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.544A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TRP H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 97 through 100 removed outlier: 7.161A pdb=" N TYR H 100F" --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.506A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.562A pdb=" N ARG L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 62 through 67 removed outlier: 4.240A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1251 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: 3.42 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6199 1.34 - 1.47: 5207 1.47 - 1.59: 8082 1.59 - 1.71: 0 1.71 - 1.84: 159 Bond restraints: 19647 Sorted by residual: bond pdb=" C HIS B 28 " pdb=" N SER B 29 " ideal model delta sigma weight residual 1.329 1.256 0.073 1.86e-02 2.89e+03 1.54e+01 bond pdb=" N ARG B 13 " pdb=" CA ARG B 13 " ideal model delta sigma weight residual 1.456 1.427 0.030 1.04e-02 9.25e+03 8.13e+00 bond pdb=" CB PRO F 142 " pdb=" CG PRO F 142 " ideal model delta sigma weight residual 1.492 1.352 0.140 5.00e-02 4.00e+02 7.82e+00 bond pdb=" C VAL E 231 " pdb=" N PRO E 232 " ideal model delta sigma weight residual 1.335 1.311 0.024 8.70e-03 1.32e+04 7.57e+00 bond pdb=" N GLN C 196 " pdb=" CA GLN C 196 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.80e+00 ... (remaining 19642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 24915 1.68 - 3.36: 1523 3.36 - 5.04: 236 5.04 - 6.73: 58 6.73 - 8.41: 10 Bond angle restraints: 26742 Sorted by residual: angle pdb=" N TYR F 360 " pdb=" CA TYR F 360 " pdb=" C TYR F 360 " ideal model delta sigma weight residual 113.88 107.87 6.01 1.23e+00 6.61e-01 2.39e+01 angle pdb=" N GLY D 325 " pdb=" CA GLY D 325 " pdb=" C GLY D 325 " ideal model delta sigma weight residual 110.88 117.59 -6.71 1.48e+00 4.57e-01 2.06e+01 angle pdb=" C TYR E 262 " pdb=" N THR E 263 " pdb=" CA THR E 263 " ideal model delta sigma weight residual 122.15 129.54 -7.39 1.74e+00 3.30e-01 1.81e+01 angle pdb=" C ILE A 369 " pdb=" N CYS A 370 " pdb=" CA CYS A 370 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" CA TYR F 9 " pdb=" CB TYR F 9 " pdb=" CG TYR F 9 " ideal model delta sigma weight residual 113.90 120.77 -6.87 1.80e+00 3.09e-01 1.46e+01 ... (remaining 26737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 11353 17.56 - 35.12: 386 35.12 - 52.69: 67 52.69 - 70.25: 6 70.25 - 87.81: 9 Dihedral angle restraints: 11821 sinusoidal: 4637 harmonic: 7184 Sorted by residual: dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 123 " pdb=" CB CYS D 123 " ideal model delta sinusoidal sigma weight residual -86.00 -173.81 87.81 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS B 19 " pdb=" SG CYS B 19 " pdb=" SG CYS B 123 " pdb=" CB CYS B 123 " ideal model delta sinusoidal sigma weight residual -86.00 -170.94 84.94 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS C 62 " pdb=" SG CYS C 62 " pdb=" SG CYS C 94 " pdb=" CB CYS C 94 " ideal model delta sinusoidal sigma weight residual -86.00 -162.15 76.15 1 1.00e+01 1.00e-02 7.30e+01 ... (remaining 11818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1615 0.040 - 0.079: 869 0.079 - 0.119: 360 0.119 - 0.158: 83 0.158 - 0.198: 8 Chirality restraints: 2935 Sorted by residual: chirality pdb=" CB ILE A 369 " pdb=" CA ILE A 369 " pdb=" CG1 ILE A 369 " pdb=" CG2 ILE A 369 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CB VAL E 148 " pdb=" CA VAL E 148 " pdb=" CG1 VAL E 148 " pdb=" CG2 VAL E 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CB ILE F 31 " pdb=" CA ILE F 31 " pdb=" CG1 ILE F 31 " pdb=" CG2 ILE F 31 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 2932 not shown) Planarity restraints: 3462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 57 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO A 58 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 39 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO C 40 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 9 " -0.031 2.00e-02 2.50e+03 1.80e-02 6.45e+00 pdb=" CG TYR F 9 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 9 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR F 9 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR F 9 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 9 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR F 9 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR F 9 " -0.007 2.00e-02 2.50e+03 ... (remaining 3459 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 179 2.58 - 3.16: 15668 3.16 - 3.74: 26997 3.74 - 4.32: 38718 4.32 - 4.90: 66294 Nonbonded interactions: 147856 Sorted by model distance: nonbonded pdb=" OG1 THR D 297 " pdb=" OG1 THR D 307 " model vdw 1.997 3.040 nonbonded pdb=" O CYS B 22 " pdb=" OG SER B 122 " model vdw 2.005 3.040 nonbonded pdb=" OG SER E 309 " pdb=" OD1 ASP E 311 " model vdw 2.051 3.040 nonbonded pdb=" OG SER F 185 " pdb=" O PHE F 217 " model vdw 2.082 3.040 nonbonded pdb=" OG SER E 205 " pdb=" OG SER E 210 " model vdw 2.082 3.040 ... (remaining 147851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 320 or resid 324 through 344 or resid 352 throug \ h 396)) selection = (chain 'C' and resid 2 through 396) selection = (chain 'E' and (resid 2 through 320 or resid 324 through 344 or resid 352 throug \ h 396)) } ncs_group { reference = (chain 'B' and resid 6 through 344) selection = (chain 'D' and (resid 6 through 201 or resid 205 through 344)) selection = (chain 'F' and (resid 6 through 201 or resid 205 through 344)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.620 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 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 : 0.012 0.140 19687 Z= 0.488 Angle : 0.940 8.408 26822 Z= 0.521 Chirality : 0.054 0.198 2935 Planarity : 0.008 0.067 3462 Dihedral : 9.271 75.806 7101 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.92 % Favored : 88.92 % Rotamer: Outliers : 0.05 % Allowed : 1.00 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.71 (0.14), residues: 2445 helix: -4.63 (0.24), residues: 60 sheet: -2.45 (0.15), residues: 915 loop : -3.68 (0.12), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 67 TYR 0.038 0.003 TYR F 9 PHE 0.030 0.003 PHE F 328 TRP 0.020 0.003 TRP D 236 HIS 0.018 0.003 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.01156 (19647) covalent geometry : angle 0.93528 (26742) SS BOND : bond 0.00610 ( 40) SS BOND : angle 1.89068 ( 80) hydrogen bonds : bond 0.15821 ( 493) hydrogen bonds : angle 8.35173 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 824 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7754 (t) cc_final: 0.7526 (t) REVERT: A 29 ILE cc_start: 0.8507 (mt) cc_final: 0.8250 (mm) REVERT: A 30 SER cc_start: 0.8029 (m) cc_final: 0.7408 (p) REVERT: A 35 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7620 (ttmm) REVERT: A 37 LYS cc_start: 0.8302 (mttt) cc_final: 0.7979 (mtmm) REVERT: A 45 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6627 (mm-30) REVERT: A 51 TYR cc_start: 0.7251 (p90) cc_final: 0.6668 (p90) REVERT: A 52 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8139 (ttpp) REVERT: A 105 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7853 (mtpp) REVERT: A 111 SER cc_start: 0.7953 (t) cc_final: 0.7731 (p) REVERT: A 136 THR cc_start: 0.7292 (m) cc_final: 0.6849 (p) REVERT: A 137 VAL cc_start: 0.8122 (t) cc_final: 0.7732 (p) REVERT: A 145 THR cc_start: 0.8367 (m) cc_final: 0.8063 (t) REVERT: A 147 TYR cc_start: 0.7575 (m-10) cc_final: 0.7001 (m-80) REVERT: A 176 LYS cc_start: 0.8132 (mttt) cc_final: 0.7894 (mtpp) REVERT: A 179 GLN cc_start: 0.7775 (tt0) cc_final: 0.7412 (tt0) REVERT: A 189 PHE cc_start: 0.7878 (p90) cc_final: 0.7673 (p90) REVERT: A 238 SER cc_start: 0.7327 (t) cc_final: 0.6853 (p) REVERT: A 252 LYS cc_start: 0.8758 (tttt) cc_final: 0.8450 (ttmm) REVERT: A 269 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 281 ASP cc_start: 0.7881 (t0) cc_final: 0.7545 (t0) REVERT: A 284 ASP cc_start: 0.7037 (m-30) cc_final: 0.6829 (m-30) REVERT: A 291 SER cc_start: 0.8305 (p) cc_final: 0.8031 (t) REVERT: A 308 TYR cc_start: 0.7645 (p90) cc_final: 0.7440 (p90) REVERT: A 340 LYS cc_start: 0.8151 (tttt) cc_final: 0.7928 (ttmt) REVERT: B 42 ASP cc_start: 0.5781 (p0) cc_final: 0.5510 (p0) REVERT: B 62 LYS cc_start: 0.7105 (tttt) cc_final: 0.6747 (ttmm) REVERT: B 108 ASP cc_start: 0.7311 (p0) cc_final: 0.6917 (p0) REVERT: B 115 LYS cc_start: 0.7516 (mtpt) cc_final: 0.7163 (mtpp) REVERT: B 130 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7130 (mtmm) REVERT: B 164 TYR cc_start: 0.7949 (m-80) cc_final: 0.7463 (m-80) REVERT: B 192 ASP cc_start: 0.7117 (t70) cc_final: 0.6853 (t70) REVERT: B 235 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8115 (mmtp) REVERT: B 254 LYS cc_start: 0.7415 (mmmt) cc_final: 0.7194 (mmmt) REVERT: B 324 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7474 (mtmm) REVERT: B 336 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7826 (ttmm) REVERT: C 19 VAL cc_start: 0.7959 (t) cc_final: 0.7709 (m) REVERT: C 29 ILE cc_start: 0.7984 (mt) cc_final: 0.7769 (mm) REVERT: C 35 LYS cc_start: 0.8470 (tttt) cc_final: 0.8031 (tmtt) REVERT: C 76 GLU cc_start: 0.7458 (tp30) cc_final: 0.6943 (tp30) REVERT: C 79 LYS cc_start: 0.8101 (tmtm) cc_final: 0.7424 (tmtm) REVERT: C 105 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7440 (tttp) REVERT: C 107 TYR cc_start: 0.7506 (p90) cc_final: 0.7302 (p90) REVERT: C 120 GLU cc_start: 0.7540 (pt0) cc_final: 0.7273 (pt0) REVERT: C 128 SER cc_start: 0.7797 (m) cc_final: 0.6964 (p) REVERT: C 130 GLN cc_start: 0.7817 (tt0) cc_final: 0.7467 (mt0) REVERT: C 185 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5562 (m-10) REVERT: C 220 VAL cc_start: 0.8325 (t) cc_final: 0.8073 (m) REVERT: C 244 LYS cc_start: 0.8033 (mtpm) cc_final: 0.7800 (mttm) REVERT: C 245 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7436 (mtpt) REVERT: C 246 ASP cc_start: 0.6700 (m-30) cc_final: 0.6291 (m-30) REVERT: C 254 THR cc_start: 0.8393 (p) cc_final: 0.8170 (t) REVERT: C 261 ILE cc_start: 0.8034 (mm) cc_final: 0.7791 (mm) REVERT: C 340 LYS cc_start: 0.4836 (tttt) cc_final: 0.3924 (tttp) REVERT: C 355 HIS cc_start: 0.7011 (m-70) cc_final: 0.6737 (m-70) REVERT: C 392 GLN cc_start: 0.7776 (mt0) cc_final: 0.7558 (mt0) REVERT: D 31 ILE cc_start: 0.7777 (tt) cc_final: 0.7546 (tt) REVERT: D 74 ILE cc_start: 0.8059 (mt) cc_final: 0.7859 (mt) REVERT: D 75 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8183 (mttm) REVERT: D 77 ILE cc_start: 0.8299 (mt) cc_final: 0.7887 (tt) REVERT: D 83 SER cc_start: 0.7954 (m) cc_final: 0.7686 (p) REVERT: D 94 ASP cc_start: 0.6972 (t0) cc_final: 0.6645 (t0) REVERT: D 100 LEU cc_start: 0.8476 (tp) cc_final: 0.8111 (tp) REVERT: D 108 ASP cc_start: 0.7282 (m-30) cc_final: 0.7070 (m-30) REVERT: D 130 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7558 (mtmm) REVERT: D 134 VAL cc_start: 0.8444 (t) cc_final: 0.8221 (t) REVERT: D 173 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6988 (mm-30) REVERT: D 180 SER cc_start: 0.7634 (p) cc_final: 0.7312 (m) REVERT: D 254 LYS cc_start: 0.8598 (mtmp) cc_final: 0.8194 (mtpp) REVERT: D 277 THR cc_start: 0.8113 (m) cc_final: 0.7723 (p) REVERT: D 309 GLU cc_start: 0.7337 (tt0) cc_final: 0.7051 (tt0) REVERT: E 6 THR cc_start: 0.8113 (m) cc_final: 0.7788 (p) REVERT: E 9 SER cc_start: 0.8377 (t) cc_final: 0.8172 (t) REVERT: E 17 THR cc_start: 0.7900 (t) cc_final: 0.7104 (m) REVERT: E 18 ILE cc_start: 0.8600 (pt) cc_final: 0.8388 (mm) REVERT: E 35 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7656 (mtpp) REVERT: E 69 THR cc_start: 0.7375 (p) cc_final: 0.7002 (t) REVERT: E 79 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7584 (ttmm) REVERT: E 202 ASP cc_start: 0.7856 (p0) cc_final: 0.7598 (p0) REVERT: E 246 ASP cc_start: 0.6914 (m-30) cc_final: 0.6700 (m-30) REVERT: E 252 LYS cc_start: 0.7962 (tttt) cc_final: 0.7610 (ptmm) REVERT: E 262 TYR cc_start: 0.7467 (m-80) cc_final: 0.5802 (m-80) REVERT: E 269 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6996 (mt-10) REVERT: E 300 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6988 (tm-30) REVERT: E 304 ASN cc_start: 0.8016 (m110) cc_final: 0.7606 (m-40) REVERT: E 324 LYS cc_start: 0.8122 (mtmp) cc_final: 0.7674 (mtmm) REVERT: E 340 LYS cc_start: 0.7583 (tttt) cc_final: 0.7265 (ttmt) REVERT: E 349 GLN cc_start: 0.7153 (tp40) cc_final: 0.6694 (tp40) REVERT: E 392 GLN cc_start: 0.7583 (mp10) cc_final: 0.7298 (mp10) REVERT: F 8 GLU cc_start: 0.7427 (tp30) cc_final: 0.7117 (tp30) REVERT: F 12 THR cc_start: 0.8053 (m) cc_final: 0.7824 (m) REVERT: F 57 SER cc_start: 0.8409 (p) cc_final: 0.8065 (t) REVERT: F 60 ASN cc_start: 0.7877 (m-40) cc_final: 0.7413 (m-40) REVERT: F 75 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7692 (mmtp) REVERT: F 100 LEU cc_start: 0.8177 (tp) cc_final: 0.7973 (tt) REVERT: F 130 LYS cc_start: 0.7873 (pttm) cc_final: 0.7535 (ptpp) REVERT: F 210 THR cc_start: 0.6934 (m) cc_final: 0.6612 (p) REVERT: F 222 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7410 (mtpp) REVERT: F 235 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7738 (mtpp) REVERT: F 245 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7885 (ptmt) REVERT: F 290 LYS cc_start: 0.7564 (mttt) cc_final: 0.7285 (mttt) REVERT: F 347 ASN cc_start: 0.8194 (t0) cc_final: 0.7867 (t0) REVERT: L 7 SER cc_start: 0.7339 (t) cc_final: 0.6916 (p) REVERT: L 20 THR cc_start: 0.8610 (t) cc_final: 0.8324 (p) REVERT: L 42 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8070 (mmmt) REVERT: L 77 SER cc_start: 0.7576 (t) cc_final: 0.7140 (m) REVERT: L 82 ASP cc_start: 0.7502 (m-30) cc_final: 0.7261 (m-30) REVERT: L 104 VAL cc_start: 0.7899 (t) cc_final: 0.7512 (p) outliers start: 1 outliers final: 0 residues processed: 824 average time/residue: 0.1417 time to fit residues: 171.2686 Evaluate side-chains 714 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 713 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 77 GLN A 100 ASN A 216 ASN A 222 GLN B 81 GLN B 256 HIS B 332 ASN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN C 222 GLN D 71 HIS D 288 HIS E 157 ASN E 362 HIS ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 HIS F 132 ASN F 156 HIS F 305 HIS F 318 ASN L 37 GLN L 38 GLN L 90 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108717 restraints weight = 30127.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111680 restraints weight = 12737.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113410 restraints weight = 6582.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114452 restraints weight = 3993.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115107 restraints weight = 2797.552| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19687 Z= 0.172 Angle : 0.664 8.513 26822 Z= 0.349 Chirality : 0.047 0.207 2935 Planarity : 0.006 0.050 3462 Dihedral : 6.002 30.724 2676 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.99 % Favored : 92.92 % Rotamer: Outliers : 1.52 % Allowed : 8.85 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.57 (0.15), residues: 2445 helix: -3.36 (0.48), residues: 48 sheet: -1.86 (0.15), residues: 939 loop : -2.79 (0.14), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 21 TYR 0.025 0.002 TYR A 122 PHE 0.020 0.002 PHE C 287 TRP 0.015 0.002 TRP D 236 HIS 0.008 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00395 (19647) covalent geometry : angle 0.66139 (26742) SS BOND : bond 0.00331 ( 40) SS BOND : angle 1.21591 ( 80) hydrogen bonds : bond 0.03608 ( 493) hydrogen bonds : angle 5.96112 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 738 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7680 (t) cc_final: 0.7400 (t) REVERT: A 29 ILE cc_start: 0.8631 (mt) cc_final: 0.8394 (mp) REVERT: A 30 SER cc_start: 0.8342 (m) cc_final: 0.7724 (p) REVERT: A 35 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7559 (ttmm) REVERT: A 37 LYS cc_start: 0.8248 (mttt) cc_final: 0.8027 (mtmm) REVERT: A 42 VAL cc_start: 0.8321 (t) cc_final: 0.7824 (m) REVERT: A 45 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6748 (mm-30) REVERT: A 52 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7957 (ttpp) REVERT: A 76 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6128 (tm-30) REVERT: A 82 THR cc_start: 0.7630 (m) cc_final: 0.7349 (p) REVERT: A 105 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7783 (mtpp) REVERT: A 111 SER cc_start: 0.8001 (t) cc_final: 0.7428 (t) REVERT: A 123 LYS cc_start: 0.7742 (mtmt) cc_final: 0.7390 (mtmt) REVERT: A 130 GLN cc_start: 0.7512 (tt0) cc_final: 0.6999 (tt0) REVERT: A 137 VAL cc_start: 0.8150 (t) cc_final: 0.7782 (p) REVERT: A 147 TYR cc_start: 0.7649 (m-10) cc_final: 0.7138 (m-80) REVERT: A 176 LYS cc_start: 0.8176 (mttt) cc_final: 0.7816 (mtpp) REVERT: A 205 SER cc_start: 0.8542 (t) cc_final: 0.8168 (p) REVERT: A 218 ASN cc_start: 0.7828 (t0) cc_final: 0.7617 (t0) REVERT: A 235 GLN cc_start: 0.7620 (pt0) cc_final: 0.7230 (pt0) REVERT: A 252 LYS cc_start: 0.8767 (tttt) cc_final: 0.8531 (ttmm) REVERT: A 269 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6562 (mt-10) REVERT: A 281 ASP cc_start: 0.7778 (t0) cc_final: 0.7472 (t0) REVERT: A 284 ASP cc_start: 0.6964 (m-30) cc_final: 0.6725 (m-30) REVERT: A 291 SER cc_start: 0.8281 (p) cc_final: 0.8076 (t) REVERT: A 300 GLU cc_start: 0.7132 (pt0) cc_final: 0.6868 (pt0) REVERT: A 307 VAL cc_start: 0.8766 (t) cc_final: 0.8503 (p) REVERT: A 339 LEU cc_start: 0.8661 (mp) cc_final: 0.8439 (mt) REVERT: A 368 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 377 LYS cc_start: 0.7714 (mttp) cc_final: 0.7490 (mttp) REVERT: B 34 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7030 (mm-30) REVERT: B 37 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7208 (mttt) REVERT: B 39 ASP cc_start: 0.7461 (m-30) cc_final: 0.7225 (m-30) REVERT: B 68 TYR cc_start: 0.8661 (p90) cc_final: 0.8354 (p90) REVERT: B 108 ASP cc_start: 0.7370 (p0) cc_final: 0.6976 (p0) REVERT: B 115 LYS cc_start: 0.7513 (mtpt) cc_final: 0.7287 (mtpp) REVERT: B 164 TYR cc_start: 0.8112 (m-80) cc_final: 0.7743 (m-80) REVERT: B 175 ASP cc_start: 0.6808 (t0) cc_final: 0.6512 (t0) REVERT: B 192 ASP cc_start: 0.7037 (t70) cc_final: 0.6823 (t70) REVERT: B 230 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7894 (mtp85) REVERT: B 254 LYS cc_start: 0.7409 (mmmt) cc_final: 0.6801 (mmmt) REVERT: B 294 TYR cc_start: 0.7706 (m-10) cc_final: 0.7257 (m-80) REVERT: B 324 LYS cc_start: 0.7625 (mtmm) cc_final: 0.7365 (mtmm) REVERT: B 336 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7857 (ttmm) REVERT: C 26 PRO cc_start: 0.7844 (Cg_exo) cc_final: 0.7618 (Cg_endo) REVERT: C 35 LYS cc_start: 0.8317 (tttt) cc_final: 0.7830 (tttm) REVERT: C 75 ASP cc_start: 0.7424 (t0) cc_final: 0.6918 (t0) REVERT: C 87 PHE cc_start: 0.7655 (m-10) cc_final: 0.7365 (m-80) REVERT: C 104 SER cc_start: 0.8003 (m) cc_final: 0.7778 (t) REVERT: C 120 GLU cc_start: 0.7681 (pt0) cc_final: 0.7409 (pt0) REVERT: C 185 TYR cc_start: 0.7965 (m-80) cc_final: 0.7716 (m-80) REVERT: C 186 ASN cc_start: 0.8102 (m110) cc_final: 0.7770 (m110) REVERT: C 242 GLN cc_start: 0.7595 (tp40) cc_final: 0.7209 (tp-100) REVERT: C 245 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7497 (mtpt) REVERT: C 246 ASP cc_start: 0.6841 (m-30) cc_final: 0.6501 (m-30) REVERT: C 254 THR cc_start: 0.8433 (p) cc_final: 0.8139 (t) REVERT: C 261 ILE cc_start: 0.8192 (mm) cc_final: 0.7795 (mm) REVERT: C 269 GLU cc_start: 0.7177 (pt0) cc_final: 0.6740 (pt0) REVERT: C 334 SER cc_start: 0.8600 (t) cc_final: 0.8183 (p) REVERT: C 392 GLN cc_start: 0.7731 (mt0) cc_final: 0.7519 (mt0) REVERT: D 31 ILE cc_start: 0.8069 (tt) cc_final: 0.7743 (tt) REVERT: D 64 ARG cc_start: 0.7219 (mmm-85) cc_final: 0.6892 (mtp85) REVERT: D 74 ILE cc_start: 0.8186 (mt) cc_final: 0.7929 (mt) REVERT: D 75 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8169 (mttm) REVERT: D 77 ILE cc_start: 0.8371 (mt) cc_final: 0.8020 (tt) REVERT: D 82 VAL cc_start: 0.8687 (t) cc_final: 0.8425 (p) REVERT: D 94 ASP cc_start: 0.7000 (t0) cc_final: 0.6768 (t0) REVERT: D 130 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7416 (mtmm) REVERT: D 134 VAL cc_start: 0.8580 (t) cc_final: 0.8330 (t) REVERT: D 180 SER cc_start: 0.7957 (p) cc_final: 0.7513 (m) REVERT: D 215 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7600 (ttmm) REVERT: D 241 ASP cc_start: 0.7711 (p0) cc_final: 0.7510 (p0) REVERT: D 242 LYS cc_start: 0.8086 (mttm) cc_final: 0.7763 (mttp) REVERT: D 254 LYS cc_start: 0.8522 (mtmp) cc_final: 0.8201 (mtpp) REVERT: D 277 THR cc_start: 0.8289 (m) cc_final: 0.7927 (p) REVERT: D 286 LYS cc_start: 0.7883 (tptm) cc_final: 0.7548 (tptm) REVERT: D 316 VAL cc_start: 0.8739 (p) cc_final: 0.8522 (t) REVERT: D 338 PHE cc_start: 0.8157 (m-10) cc_final: 0.7855 (m-80) REVERT: E 6 THR cc_start: 0.8071 (m) cc_final: 0.7686 (p) REVERT: E 9 SER cc_start: 0.8446 (t) cc_final: 0.8167 (t) REVERT: E 15 TYR cc_start: 0.7260 (t80) cc_final: 0.6963 (t80) REVERT: E 47 VAL cc_start: 0.8395 (m) cc_final: 0.8038 (p) REVERT: E 110 LYS cc_start: 0.8399 (ptpp) cc_final: 0.8190 (ptmm) REVERT: E 123 LYS cc_start: 0.8432 (mttt) cc_final: 0.8203 (mttt) REVERT: E 157 ASN cc_start: 0.7759 (t0) cc_final: 0.7543 (t0) REVERT: E 188 ASP cc_start: 0.6967 (t70) cc_final: 0.6584 (t70) REVERT: E 202 ASP cc_start: 0.7992 (p0) cc_final: 0.7746 (p0) REVERT: E 222 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7648 (mt0) REVERT: E 246 ASP cc_start: 0.7122 (m-30) cc_final: 0.6736 (m-30) REVERT: E 252 LYS cc_start: 0.8064 (tttt) cc_final: 0.7783 (ptmm) REVERT: E 262 TYR cc_start: 0.7609 (m-80) cc_final: 0.6226 (m-80) REVERT: E 269 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7147 (mt-10) REVERT: E 304 ASN cc_start: 0.7987 (m110) cc_final: 0.7647 (m-40) REVERT: E 324 LYS cc_start: 0.8267 (mtmp) cc_final: 0.8010 (mtmm) REVERT: E 338 THR cc_start: 0.8424 (m) cc_final: 0.8180 (t) REVERT: E 340 LYS cc_start: 0.7628 (tttt) cc_final: 0.7335 (ttmt) REVERT: F 8 GLU cc_start: 0.7412 (tp30) cc_final: 0.7120 (tp30) REVERT: F 37 LYS cc_start: 0.7567 (mmtt) cc_final: 0.7235 (mmtm) REVERT: F 53 TYR cc_start: 0.8211 (m-80) cc_final: 0.7744 (m-80) REVERT: F 57 SER cc_start: 0.8422 (p) cc_final: 0.8131 (t) REVERT: F 60 ASN cc_start: 0.7957 (m-40) cc_final: 0.7633 (m-40) REVERT: F 69 ASP cc_start: 0.7522 (t70) cc_final: 0.7240 (t70) REVERT: F 75 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7759 (mmtp) REVERT: F 120 ARG cc_start: 0.7273 (ptp-110) cc_final: 0.7057 (ttm-80) REVERT: F 129 VAL cc_start: 0.8158 (t) cc_final: 0.7832 (p) REVERT: F 175 ASP cc_start: 0.8238 (t0) cc_final: 0.7846 (t0) REVERT: F 177 SER cc_start: 0.8768 (m) cc_final: 0.8455 (p) REVERT: F 215 LYS cc_start: 0.8154 (tttt) cc_final: 0.7810 (tttp) REVERT: F 254 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7733 (mtmt) REVERT: F 261 LEU cc_start: 0.8612 (tp) cc_final: 0.8337 (mt) REVERT: F 290 LYS cc_start: 0.7558 (mttt) cc_final: 0.7295 (mttt) REVERT: F 347 ASN cc_start: 0.8394 (t0) cc_final: 0.8073 (t0) REVERT: H 39 GLN cc_start: 0.8224 (tt0) cc_final: 0.7841 (tt0) REVERT: H 76 ASN cc_start: 0.6284 (p0) cc_final: 0.5696 (p0) REVERT: H 85 GLU cc_start: 0.8061 (tp30) cc_final: 0.7723 (tp30) REVERT: H 103 TRP cc_start: 0.7967 (m100) cc_final: 0.7691 (m100) REVERT: L 4 MET cc_start: 0.6407 (mmt) cc_final: 0.6205 (mmt) REVERT: L 20 THR cc_start: 0.8576 (t) cc_final: 0.8276 (p) REVERT: L 42 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7983 (mmmt) REVERT: L 104 VAL cc_start: 0.8078 (t) cc_final: 0.7788 (p) outliers start: 32 outliers final: 20 residues processed: 757 average time/residue: 0.1386 time to fit residues: 154.4162 Evaluate side-chains 726 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 706 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain L residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 178 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 112 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 155 ASN A 235 GLN A 270 ASN B 288 HIS B 333 HIS ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS D 160 ASN D 288 HIS E 360 ASN F 52 GLN F 81 GLN F 132 ASN F 305 HIS F 318 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105859 restraints weight = 30531.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108859 restraints weight = 12894.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110633 restraints weight = 6670.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111721 restraints weight = 4028.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112376 restraints weight = 2796.285| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19687 Z= 0.191 Angle : 0.642 8.123 26822 Z= 0.336 Chirality : 0.046 0.169 2935 Planarity : 0.005 0.045 3462 Dihedral : 5.706 29.106 2674 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.98 % Favored : 91.94 % Rotamer: Outliers : 3.14 % Allowed : 12.18 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -2.87 (0.16), residues: 2445 helix: -2.69 (0.57), residues: 48 sheet: -1.26 (0.17), residues: 906 loop : -2.39 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 73 TYR 0.020 0.002 TYR A 122 PHE 0.023 0.002 PHE C 356 TRP 0.014 0.002 TRP H 103 HIS 0.006 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00434 (19647) covalent geometry : angle 0.63919 (26742) SS BOND : bond 0.00405 ( 40) SS BOND : angle 1.24901 ( 80) hydrogen bonds : bond 0.03541 ( 493) hydrogen bonds : angle 5.53970 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 693 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7671 (t) cc_final: 0.7361 (t) REVERT: A 18 ILE cc_start: 0.8281 (pt) cc_final: 0.8032 (mm) REVERT: A 30 SER cc_start: 0.8222 (m) cc_final: 0.7726 (p) REVERT: A 35 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7490 (ttmm) REVERT: A 37 LYS cc_start: 0.8268 (mttt) cc_final: 0.7723 (mtmm) REVERT: A 42 VAL cc_start: 0.8634 (t) cc_final: 0.8185 (m) REVERT: A 45 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 52 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8058 (ttpp) REVERT: A 75 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: A 76 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6253 (tm-30) REVERT: A 99 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 105 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7794 (mtpp) REVERT: A 108 VAL cc_start: 0.8909 (t) cc_final: 0.8371 (m) REVERT: A 111 SER cc_start: 0.8199 (t) cc_final: 0.7724 (t) REVERT: A 123 LYS cc_start: 0.7780 (mtmt) cc_final: 0.7456 (mtmt) REVERT: A 130 GLN cc_start: 0.7499 (tt0) cc_final: 0.7254 (tt0) REVERT: A 147 TYR cc_start: 0.7710 (m-10) cc_final: 0.7241 (m-10) REVERT: A 176 LYS cc_start: 0.8261 (mttt) cc_final: 0.7935 (mtpp) REVERT: A 205 SER cc_start: 0.8554 (t) cc_final: 0.8118 (p) REVERT: A 218 ASN cc_start: 0.7912 (t0) cc_final: 0.7686 (t0) REVERT: A 241 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6698 (tm-30) REVERT: A 269 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6528 (mt-10) REVERT: A 281 ASP cc_start: 0.7764 (t0) cc_final: 0.7499 (t0) REVERT: A 307 VAL cc_start: 0.8743 (t) cc_final: 0.8498 (p) REVERT: A 368 GLN cc_start: 0.7139 (tm-30) cc_final: 0.6870 (tm-30) REVERT: B 34 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7010 (mm-30) REVERT: B 37 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7253 (mmtt) REVERT: B 44 TYR cc_start: 0.8073 (m-80) cc_final: 0.7446 (m-80) REVERT: B 62 LYS cc_start: 0.7363 (tttt) cc_final: 0.6947 (mtpp) REVERT: B 68 TYR cc_start: 0.8686 (p90) cc_final: 0.8368 (p90) REVERT: B 108 ASP cc_start: 0.7405 (p0) cc_final: 0.7016 (p0) REVERT: B 115 LYS cc_start: 0.7554 (mtpt) cc_final: 0.7345 (mtpp) REVERT: B 159 GLN cc_start: 0.7924 (mt0) cc_final: 0.7697 (mt0) REVERT: B 164 TYR cc_start: 0.8218 (m-80) cc_final: 0.7712 (m-80) REVERT: B 175 ASP cc_start: 0.6947 (t0) cc_final: 0.6554 (t0) REVERT: B 213 LYS cc_start: 0.8092 (mttp) cc_final: 0.7871 (mmtm) REVERT: B 230 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7992 (ttm110) REVERT: B 254 LYS cc_start: 0.7512 (mmmt) cc_final: 0.6848 (mmmt) REVERT: B 265 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7305 (mmtt) REVERT: B 294 TYR cc_start: 0.8052 (m-10) cc_final: 0.7654 (m-10) REVERT: B 324 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7413 (mtmm) REVERT: B 336 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7906 (ttmm) REVERT: C 10 GLN cc_start: 0.7503 (tt0) cc_final: 0.7165 (tm-30) REVERT: C 35 LYS cc_start: 0.8383 (tttt) cc_final: 0.7908 (tttm) REVERT: C 76 GLU cc_start: 0.7721 (tp30) cc_final: 0.7142 (tp30) REVERT: C 77 GLN cc_start: 0.7419 (tp-100) cc_final: 0.7079 (tp40) REVERT: C 110 LYS cc_start: 0.8325 (ptpp) cc_final: 0.8098 (ptmt) REVERT: C 117 ASP cc_start: 0.7396 (t70) cc_final: 0.7174 (t70) REVERT: C 132 PHE cc_start: 0.7626 (m-10) cc_final: 0.7401 (m-10) REVERT: C 186 ASN cc_start: 0.8187 (m110) cc_final: 0.7863 (m110) REVERT: C 207 THR cc_start: 0.7988 (t) cc_final: 0.7716 (p) REVERT: C 222 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: C 242 GLN cc_start: 0.7667 (tp40) cc_final: 0.7215 (tp-100) REVERT: C 245 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7517 (mtpt) REVERT: C 246 ASP cc_start: 0.6816 (m-30) cc_final: 0.6589 (m-30) REVERT: C 254 THR cc_start: 0.8498 (p) cc_final: 0.8208 (t) REVERT: C 261 ILE cc_start: 0.8315 (mm) cc_final: 0.7903 (mm) REVERT: C 334 SER cc_start: 0.8589 (t) cc_final: 0.8143 (p) REVERT: D 56 ASP cc_start: 0.7782 (p0) cc_final: 0.7559 (p0) REVERT: D 64 ARG cc_start: 0.7265 (mmm-85) cc_final: 0.6876 (mtt-85) REVERT: D 74 ILE cc_start: 0.8215 (mt) cc_final: 0.7929 (mt) REVERT: D 75 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8019 (mttm) REVERT: D 77 ILE cc_start: 0.8407 (mt) cc_final: 0.8040 (tt) REVERT: D 82 VAL cc_start: 0.8731 (t) cc_final: 0.8452 (p) REVERT: D 94 ASP cc_start: 0.6822 (t0) cc_final: 0.6606 (t0) REVERT: D 130 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7487 (mtmm) REVERT: D 180 SER cc_start: 0.8115 (p) cc_final: 0.7589 (m) REVERT: D 241 ASP cc_start: 0.7780 (p0) cc_final: 0.7434 (p0) REVERT: D 242 LYS cc_start: 0.8169 (mttm) cc_final: 0.7840 (mttp) REVERT: D 254 LYS cc_start: 0.8611 (mtmp) cc_final: 0.8235 (mtpp) REVERT: D 261 LEU cc_start: 0.8688 (tp) cc_final: 0.7955 (mt) REVERT: D 277 THR cc_start: 0.8320 (m) cc_final: 0.7901 (p) REVERT: D 286 LYS cc_start: 0.8009 (tptm) cc_final: 0.7668 (tptm) REVERT: D 316 VAL cc_start: 0.8744 (p) cc_final: 0.8507 (t) REVERT: D 338 PHE cc_start: 0.8114 (m-10) cc_final: 0.7886 (m-80) REVERT: E 6 THR cc_start: 0.8153 (m) cc_final: 0.7746 (p) REVERT: E 15 TYR cc_start: 0.7322 (t80) cc_final: 0.7070 (t80) REVERT: E 47 VAL cc_start: 0.8267 (m) cc_final: 0.7942 (p) REVERT: E 110 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8173 (ptpp) REVERT: E 188 ASP cc_start: 0.6991 (t70) cc_final: 0.6597 (t70) REVERT: E 202 ASP cc_start: 0.8169 (p0) cc_final: 0.7937 (p0) REVERT: E 222 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7663 (mt0) REVERT: E 246 ASP cc_start: 0.7108 (m-30) cc_final: 0.6769 (m-30) REVERT: E 269 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7084 (mt-10) REVERT: E 280 PHE cc_start: 0.8412 (m-10) cc_final: 0.7993 (m-10) REVERT: E 324 LYS cc_start: 0.8264 (mtmp) cc_final: 0.8045 (mtmm) REVERT: E 338 THR cc_start: 0.8538 (m) cc_final: 0.8303 (t) REVERT: E 340 LYS cc_start: 0.7743 (tttt) cc_final: 0.7422 (ttmt) REVERT: E 377 LYS cc_start: 0.6838 (mtpm) cc_final: 0.6581 (mtpm) REVERT: E 386 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6708 (p90) REVERT: F 8 GLU cc_start: 0.7371 (tp30) cc_final: 0.7067 (tp30) REVERT: F 16 MET cc_start: 0.7941 (mtp) cc_final: 0.7701 (mtp) REVERT: F 19 CYS cc_start: 0.6767 (t) cc_final: 0.6533 (t) REVERT: F 37 LYS cc_start: 0.7494 (mmtt) cc_final: 0.7173 (mmtm) REVERT: F 53 TYR cc_start: 0.8246 (m-80) cc_final: 0.7774 (m-80) REVERT: F 57 SER cc_start: 0.8367 (p) cc_final: 0.7668 (t) REVERT: F 60 ASN cc_start: 0.8070 (m-40) cc_final: 0.7761 (m-40) REVERT: F 69 ASP cc_start: 0.7413 (t70) cc_final: 0.7108 (t70) REVERT: F 75 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7772 (mmtp) REVERT: F 76 GLU cc_start: 0.6615 (tp30) cc_final: 0.6402 (tp30) REVERT: F 120 ARG cc_start: 0.7338 (ptp-110) cc_final: 0.7103 (ttp80) REVERT: F 129 VAL cc_start: 0.8200 (t) cc_final: 0.7859 (p) REVERT: F 175 ASP cc_start: 0.8343 (t0) cc_final: 0.7907 (t0) REVERT: F 177 SER cc_start: 0.8788 (m) cc_final: 0.8506 (p) REVERT: F 215 LYS cc_start: 0.8209 (tttt) cc_final: 0.7677 (tttm) REVERT: F 261 LEU cc_start: 0.8567 (tp) cc_final: 0.8270 (mt) REVERT: F 290 LYS cc_start: 0.7657 (mttt) cc_final: 0.7379 (mttt) REVERT: F 347 ASN cc_start: 0.8544 (t0) cc_final: 0.8260 (t0) REVERT: H 76 ASN cc_start: 0.6409 (p0) cc_final: 0.5786 (p0) REVERT: L 20 THR cc_start: 0.8662 (t) cc_final: 0.8342 (p) REVERT: L 42 LYS cc_start: 0.8283 (mmmt) cc_final: 0.8025 (mmmt) REVERT: L 104 VAL cc_start: 0.8080 (t) cc_final: 0.7863 (p) outliers start: 66 outliers final: 40 residues processed: 721 average time/residue: 0.1351 time to fit residues: 143.9012 Evaluate side-chains 731 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 688 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 27 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 238 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 235 GLN A 270 ASN C 66 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 270 ASN C 360 ASN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN E 125 HIS E 242 GLN F 52 GLN F 132 ASN F 288 HIS F 305 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102783 restraints weight = 30628.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105713 restraints weight = 13421.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107490 restraints weight = 7275.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108568 restraints weight = 4606.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109261 restraints weight = 3327.490| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19687 Z= 0.168 Angle : 0.627 8.212 26822 Z= 0.325 Chirality : 0.045 0.164 2935 Planarity : 0.005 0.042 3462 Dihedral : 5.501 27.961 2674 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 3.00 % Allowed : 15.14 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -2.52 (0.16), residues: 2445 helix: -2.30 (0.61), residues: 48 sheet: -0.99 (0.17), residues: 895 loop : -2.18 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 38 TYR 0.018 0.002 TYR A 122 PHE 0.018 0.002 PHE C 156 TRP 0.012 0.002 TRP H 47 HIS 0.008 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00384 (19647) covalent geometry : angle 0.62414 (26742) SS BOND : bond 0.00308 ( 40) SS BOND : angle 1.31213 ( 80) hydrogen bonds : bond 0.03264 ( 493) hydrogen bonds : angle 5.32416 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 720 time to evaluate : 0.483 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 7 MET cc_start: 0.7172 (ptm) cc_final: 0.6969 (ptt) REVERT: A 9 SER cc_start: 0.7694 (t) cc_final: 0.7376 (t) REVERT: A 18 ILE cc_start: 0.8242 (pt) cc_final: 0.7990 (mm) REVERT: A 30 SER cc_start: 0.8211 (m) cc_final: 0.7731 (p) REVERT: A 35 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7662 (ttmm) REVERT: A 37 LYS cc_start: 0.8265 (mttt) cc_final: 0.7774 (mtmm) REVERT: A 42 VAL cc_start: 0.8589 (t) cc_final: 0.8087 (m) REVERT: A 45 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6851 (mm-30) REVERT: A 52 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8091 (ttpp) REVERT: A 76 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6328 (tm-30) REVERT: A 105 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7770 (mtpp) REVERT: A 111 SER cc_start: 0.8239 (t) cc_final: 0.7754 (t) REVERT: A 123 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7404 (mtmt) REVERT: A 130 GLN cc_start: 0.7508 (tt0) cc_final: 0.7253 (tt0) REVERT: A 147 TYR cc_start: 0.7728 (m-10) cc_final: 0.7225 (m-10) REVERT: A 157 ASN cc_start: 0.7592 (m-40) cc_final: 0.7358 (m-40) REVERT: A 176 LYS cc_start: 0.8272 (mttt) cc_final: 0.7946 (mtpp) REVERT: A 205 SER cc_start: 0.8543 (t) cc_final: 0.8110 (p) REVERT: A 218 ASN cc_start: 0.7919 (t0) cc_final: 0.7706 (t0) REVERT: A 241 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6736 (tm-30) REVERT: A 269 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6636 (mt-10) REVERT: A 281 ASP cc_start: 0.7746 (t0) cc_final: 0.7436 (t0) REVERT: A 307 VAL cc_start: 0.8695 (t) cc_final: 0.8386 (p) REVERT: A 368 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6897 (tm-30) REVERT: B 18 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7558 (ptm-80) REVERT: B 34 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7007 (mm-30) REVERT: B 37 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7148 (mmtt) REVERT: B 42 ASP cc_start: 0.6088 (p0) cc_final: 0.5575 (p0) REVERT: B 44 TYR cc_start: 0.8064 (m-80) cc_final: 0.7300 (m-80) REVERT: B 62 LYS cc_start: 0.7410 (tttt) cc_final: 0.6978 (mtpp) REVERT: B 68 TYR cc_start: 0.8684 (p90) cc_final: 0.8307 (p90) REVERT: B 108 ASP cc_start: 0.7430 (p0) cc_final: 0.7067 (p0) REVERT: B 138 LEU cc_start: 0.7996 (mm) cc_final: 0.7773 (mt) REVERT: B 159 GLN cc_start: 0.7921 (mt0) cc_final: 0.7649 (mt0) REVERT: B 164 TYR cc_start: 0.8236 (m-80) cc_final: 0.7719 (m-80) REVERT: B 213 LYS cc_start: 0.8059 (mttp) cc_final: 0.7261 (mtmm) REVERT: B 230 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7856 (ttm110) REVERT: B 254 LYS cc_start: 0.7513 (mmmt) cc_final: 0.6809 (mmmt) REVERT: B 265 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7358 (mmtt) REVERT: B 294 TYR cc_start: 0.8130 (m-10) cc_final: 0.7778 (m-10) REVERT: B 324 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7385 (mtmm) REVERT: B 336 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7890 (ttmm) REVERT: C 10 GLN cc_start: 0.7524 (tt0) cc_final: 0.7031 (tm-30) REVERT: C 35 LYS cc_start: 0.8426 (tttt) cc_final: 0.7947 (tttm) REVERT: C 105 LYS cc_start: 0.7607 (ttmt) cc_final: 0.7115 (ttmm) REVERT: C 120 GLU cc_start: 0.7626 (pt0) cc_final: 0.7145 (pt0) REVERT: C 130 GLN cc_start: 0.8292 (mt0) cc_final: 0.8057 (mt0) REVERT: C 132 PHE cc_start: 0.7703 (m-10) cc_final: 0.7362 (m-10) REVERT: C 166 LEU cc_start: 0.8432 (mt) cc_final: 0.8176 (mp) REVERT: C 186 ASN cc_start: 0.8201 (m110) cc_final: 0.7915 (m110) REVERT: C 207 THR cc_start: 0.7999 (t) cc_final: 0.7712 (p) REVERT: C 214 TYR cc_start: 0.8287 (t80) cc_final: 0.7793 (t80) REVERT: C 245 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7506 (mtpt) REVERT: C 246 ASP cc_start: 0.6853 (m-30) cc_final: 0.6644 (m-30) REVERT: C 254 THR cc_start: 0.8431 (p) cc_final: 0.8141 (t) REVERT: C 261 ILE cc_start: 0.8300 (mm) cc_final: 0.7932 (mm) REVERT: C 269 GLU cc_start: 0.7079 (pt0) cc_final: 0.6760 (pt0) REVERT: C 334 SER cc_start: 0.8572 (t) cc_final: 0.8103 (p) REVERT: C 338 THR cc_start: 0.7939 (m) cc_final: 0.7509 (t) REVERT: D 64 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6928 (mtt-85) REVERT: D 74 ILE cc_start: 0.8264 (mt) cc_final: 0.7969 (mt) REVERT: D 75 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8229 (mttm) REVERT: D 77 ILE cc_start: 0.8391 (mt) cc_final: 0.8126 (tt) REVERT: D 130 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7421 (mtmm) REVERT: D 180 SER cc_start: 0.8119 (p) cc_final: 0.7533 (m) REVERT: D 215 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7568 (ttmm) REVERT: D 242 LYS cc_start: 0.8226 (mttm) cc_final: 0.7918 (mttm) REVERT: D 261 LEU cc_start: 0.8646 (tp) cc_final: 0.8429 (mt) REVERT: D 277 THR cc_start: 0.8340 (m) cc_final: 0.7903 (p) REVERT: D 286 LYS cc_start: 0.7991 (tptm) cc_final: 0.7622 (tptm) REVERT: D 338 PHE cc_start: 0.8073 (m-10) cc_final: 0.7842 (m-80) REVERT: E 6 THR cc_start: 0.8167 (m) cc_final: 0.7727 (p) REVERT: E 15 TYR cc_start: 0.7300 (t80) cc_final: 0.7063 (t80) REVERT: E 110 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8124 (mtmm) REVERT: E 157 ASN cc_start: 0.7761 (t0) cc_final: 0.7423 (t0) REVERT: E 188 ASP cc_start: 0.7018 (t70) cc_final: 0.6593 (t70) REVERT: E 202 ASP cc_start: 0.8149 (p0) cc_final: 0.7938 (p0) REVERT: E 203 ILE cc_start: 0.8117 (mm) cc_final: 0.7826 (pt) REVERT: E 222 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7629 (mt0) REVERT: E 246 ASP cc_start: 0.7133 (m-30) cc_final: 0.6671 (m-30) REVERT: E 269 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7007 (mt-10) REVERT: E 280 PHE cc_start: 0.8436 (m-10) cc_final: 0.7964 (m-10) REVERT: E 304 ASN cc_start: 0.8027 (m110) cc_final: 0.7682 (m-40) REVERT: E 334 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8383 (p) REVERT: E 338 THR cc_start: 0.8574 (m) cc_final: 0.8300 (t) REVERT: E 340 LYS cc_start: 0.7741 (tttt) cc_final: 0.7396 (ttmt) REVERT: E 386 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.6649 (p90) REVERT: F 8 GLU cc_start: 0.7370 (tp30) cc_final: 0.7076 (tp30) REVERT: F 16 MET cc_start: 0.7969 (mtp) cc_final: 0.7724 (mtp) REVERT: F 19 CYS cc_start: 0.6755 (t) cc_final: 0.6543 (t) REVERT: F 37 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7144 (mmtm) REVERT: F 53 TYR cc_start: 0.8223 (m-80) cc_final: 0.7828 (m-80) REVERT: F 57 SER cc_start: 0.8387 (p) cc_final: 0.7766 (t) REVERT: F 60 ASN cc_start: 0.8066 (m-40) cc_final: 0.7761 (m-40) REVERT: F 69 ASP cc_start: 0.7363 (t70) cc_final: 0.7108 (t70) REVERT: F 75 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7630 (mmtp) REVERT: F 76 GLU cc_start: 0.6490 (tp30) cc_final: 0.6199 (tp30) REVERT: F 120 ARG cc_start: 0.7373 (ptp-110) cc_final: 0.7107 (ttm-80) REVERT: F 129 VAL cc_start: 0.8185 (t) cc_final: 0.7846 (p) REVERT: F 175 ASP cc_start: 0.8354 (t0) cc_final: 0.7923 (t0) REVERT: F 177 SER cc_start: 0.8776 (m) cc_final: 0.8479 (p) REVERT: F 215 LYS cc_start: 0.8197 (tttt) cc_final: 0.7793 (tttp) REVERT: F 227 ARG cc_start: 0.7379 (tpp80) cc_final: 0.7177 (mmt-90) REVERT: F 261 LEU cc_start: 0.8521 (tp) cc_final: 0.8275 (mt) REVERT: F 277 THR cc_start: 0.8172 (m) cc_final: 0.7963 (p) REVERT: F 286 LYS cc_start: 0.8263 (tppp) cc_final: 0.8009 (ttmm) REVERT: F 290 LYS cc_start: 0.7679 (mttt) cc_final: 0.7408 (mttt) REVERT: H 76 ASN cc_start: 0.6516 (p0) cc_final: 0.5765 (p0) REVERT: L 20 THR cc_start: 0.8638 (t) cc_final: 0.8325 (p) REVERT: L 42 LYS cc_start: 0.8282 (mmmt) cc_final: 0.8023 (mmmt) REVERT: L 104 VAL cc_start: 0.8096 (t) cc_final: 0.7885 (p) outliers start: 63 outliers final: 48 residues processed: 752 average time/residue: 0.1382 time to fit residues: 153.7293 Evaluate side-chains 740 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 690 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 234 optimal weight: 0.0060 chunk 42 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 241 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 130 optimal weight: 0.3980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN F 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104515 restraints weight = 30772.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107540 restraints weight = 13313.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109337 restraints weight = 7028.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110422 restraints weight = 4325.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111095 restraints weight = 3057.642| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19687 Z= 0.128 Angle : 0.604 9.948 26822 Z= 0.312 Chirality : 0.044 0.170 2935 Planarity : 0.004 0.040 3462 Dihedral : 5.264 26.747 2674 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.20 % Favored : 92.76 % Rotamer: Outliers : 3.43 % Allowed : 15.90 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -2.27 (0.16), residues: 2445 helix: -2.28 (0.62), residues: 49 sheet: -0.82 (0.17), residues: 889 loop : -1.99 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.021 0.001 TYR B 238 PHE 0.026 0.001 PHE C 356 TRP 0.011 0.001 TRP D 330 HIS 0.007 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00296 (19647) covalent geometry : angle 0.60148 (26742) SS BOND : bond 0.00256 ( 40) SS BOND : angle 1.24955 ( 80) hydrogen bonds : bond 0.03060 ( 493) hydrogen bonds : angle 5.19742 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 682 time to evaluate : 0.683 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 7 MET cc_start: 0.7233 (ptm) cc_final: 0.6945 (ptt) REVERT: A 9 SER cc_start: 0.7683 (t) cc_final: 0.7342 (t) REVERT: A 18 ILE cc_start: 0.8004 (pt) cc_final: 0.7749 (mm) REVERT: A 30 SER cc_start: 0.8127 (m) cc_final: 0.7675 (p) REVERT: A 35 LYS cc_start: 0.8446 (ttmt) cc_final: 0.7964 (ttmm) REVERT: A 37 LYS cc_start: 0.8253 (mttt) cc_final: 0.7821 (mtmm) REVERT: A 42 VAL cc_start: 0.8492 (t) cc_final: 0.7950 (m) REVERT: A 45 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6720 (mm-30) REVERT: A 52 LYS cc_start: 0.8360 (ttpt) cc_final: 0.8085 (ttpp) REVERT: A 75 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: A 76 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6285 (tm-30) REVERT: A 82 THR cc_start: 0.7591 (m) cc_final: 0.7240 (p) REVERT: A 105 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7766 (mtpp) REVERT: A 111 SER cc_start: 0.8276 (t) cc_final: 0.7831 (t) REVERT: A 123 LYS cc_start: 0.7679 (mtmt) cc_final: 0.7309 (mtmt) REVERT: A 130 GLN cc_start: 0.7498 (tt0) cc_final: 0.6949 (tt0) REVERT: A 147 TYR cc_start: 0.7758 (m-10) cc_final: 0.7142 (m-80) REVERT: A 157 ASN cc_start: 0.7368 (m-40) cc_final: 0.7135 (m-40) REVERT: A 176 LYS cc_start: 0.8271 (mttt) cc_final: 0.7955 (mtpp) REVERT: A 205 SER cc_start: 0.8516 (t) cc_final: 0.8100 (p) REVERT: A 218 ASN cc_start: 0.7972 (t0) cc_final: 0.7706 (t0) REVERT: A 241 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6576 (tm-30) REVERT: A 245 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7229 (mtpp) REVERT: A 281 ASP cc_start: 0.7734 (t0) cc_final: 0.7412 (t0) REVERT: A 368 GLN cc_start: 0.7226 (tm-30) cc_final: 0.6850 (tm-30) REVERT: B 34 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7069 (mm-30) REVERT: B 37 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7083 (mmtt) REVERT: B 44 TYR cc_start: 0.8044 (m-80) cc_final: 0.7468 (m-80) REVERT: B 62 LYS cc_start: 0.7405 (tttt) cc_final: 0.6965 (mtpp) REVERT: B 68 TYR cc_start: 0.8656 (p90) cc_final: 0.8342 (p90) REVERT: B 108 ASP cc_start: 0.7418 (p0) cc_final: 0.7020 (p0) REVERT: B 159 GLN cc_start: 0.7903 (mt0) cc_final: 0.7660 (mt0) REVERT: B 164 TYR cc_start: 0.8244 (m-80) cc_final: 0.7692 (m-80) REVERT: B 175 ASP cc_start: 0.6748 (t0) cc_final: 0.6419 (m-30) REVERT: B 230 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7824 (ttm110) REVERT: B 254 LYS cc_start: 0.7435 (mmmt) cc_final: 0.6799 (mmmt) REVERT: B 265 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7480 (mmtt) REVERT: B 324 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7336 (mtmm) REVERT: B 336 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7832 (ttmm) REVERT: C 10 GLN cc_start: 0.7516 (tt0) cc_final: 0.7281 (tm-30) REVERT: C 35 LYS cc_start: 0.8391 (tttt) cc_final: 0.7917 (tttm) REVERT: C 105 LYS cc_start: 0.7635 (ttmt) cc_final: 0.7062 (ttmm) REVERT: C 107 TYR cc_start: 0.8078 (p90) cc_final: 0.7548 (p90) REVERT: C 120 GLU cc_start: 0.7592 (pt0) cc_final: 0.7062 (pt0) REVERT: C 132 PHE cc_start: 0.7613 (m-10) cc_final: 0.7340 (m-10) REVERT: C 184 ILE cc_start: 0.8468 (mm) cc_final: 0.8035 (mm) REVERT: C 207 THR cc_start: 0.7986 (t) cc_final: 0.7699 (p) REVERT: C 214 TYR cc_start: 0.8315 (t80) cc_final: 0.7732 (t80) REVERT: C 222 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7466 (mt0) REVERT: C 245 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7507 (mtpt) REVERT: C 254 THR cc_start: 0.8421 (p) cc_final: 0.8142 (t) REVERT: C 261 ILE cc_start: 0.8289 (mm) cc_final: 0.7922 (mm) REVERT: C 266 ILE cc_start: 0.8343 (mt) cc_final: 0.8034 (mm) REVERT: C 269 GLU cc_start: 0.7123 (pt0) cc_final: 0.6774 (pt0) REVERT: C 288 THR cc_start: 0.6710 (OUTLIER) cc_final: 0.6336 (p) REVERT: C 334 SER cc_start: 0.8571 (t) cc_final: 0.8079 (p) REVERT: C 338 THR cc_start: 0.7939 (m) cc_final: 0.7543 (t) REVERT: C 358 THR cc_start: 0.8257 (t) cc_final: 0.7948 (p) REVERT: C 394 HIS cc_start: 0.7498 (p90) cc_final: 0.7233 (p90) REVERT: D 56 ASP cc_start: 0.7834 (p0) cc_final: 0.7577 (p0) REVERT: D 64 ARG cc_start: 0.7271 (mmm-85) cc_final: 0.6932 (mtt-85) REVERT: D 74 ILE cc_start: 0.8224 (mt) cc_final: 0.7877 (mt) REVERT: D 75 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8175 (mttm) REVERT: D 77 ILE cc_start: 0.8342 (mt) cc_final: 0.8097 (tt) REVERT: D 94 ASP cc_start: 0.6824 (t0) cc_final: 0.6608 (t0) REVERT: D 130 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7517 (mtmm) REVERT: D 180 SER cc_start: 0.8373 (p) cc_final: 0.7840 (m) REVERT: D 215 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7433 (ttmm) REVERT: D 241 ASP cc_start: 0.7591 (p0) cc_final: 0.7249 (p0) REVERT: D 286 LYS cc_start: 0.8074 (tptm) cc_final: 0.7809 (tptm) REVERT: D 338 PHE cc_start: 0.8066 (m-10) cc_final: 0.7829 (m-80) REVERT: D 354 GLU cc_start: 0.5264 (OUTLIER) cc_final: 0.3045 (tp30) REVERT: E 6 THR cc_start: 0.8129 (m) cc_final: 0.7720 (p) REVERT: E 15 TYR cc_start: 0.7347 (t80) cc_final: 0.7094 (t80) REVERT: E 35 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7723 (ttpp) REVERT: E 188 ASP cc_start: 0.7008 (t70) cc_final: 0.6602 (t70) REVERT: E 202 ASP cc_start: 0.8159 (p0) cc_final: 0.7950 (p0) REVERT: E 203 ILE cc_start: 0.8120 (mm) cc_final: 0.7841 (pt) REVERT: E 222 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7637 (mt0) REVERT: E 246 ASP cc_start: 0.7101 (m-30) cc_final: 0.6760 (m-30) REVERT: E 280 PHE cc_start: 0.8406 (m-10) cc_final: 0.7935 (m-10) REVERT: E 324 LYS cc_start: 0.8291 (mtmm) cc_final: 0.7901 (mtmm) REVERT: E 338 THR cc_start: 0.8575 (m) cc_final: 0.8306 (t) REVERT: E 340 LYS cc_start: 0.7699 (tttt) cc_final: 0.7380 (ttmt) REVERT: E 386 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6549 (p90) REVERT: F 8 GLU cc_start: 0.7303 (tp30) cc_final: 0.7039 (tp30) REVERT: F 16 MET cc_start: 0.7938 (mtp) cc_final: 0.7717 (mtp) REVERT: F 19 CYS cc_start: 0.6777 (t) cc_final: 0.6565 (t) REVERT: F 37 LYS cc_start: 0.7517 (mmtt) cc_final: 0.7164 (mmtm) REVERT: F 53 TYR cc_start: 0.8202 (m-80) cc_final: 0.7832 (m-80) REVERT: F 57 SER cc_start: 0.8497 (p) cc_final: 0.7899 (t) REVERT: F 60 ASN cc_start: 0.7937 (m-40) cc_final: 0.7632 (m-40) REVERT: F 69 ASP cc_start: 0.7326 (t70) cc_final: 0.7056 (t70) REVERT: F 75 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7603 (mmtp) REVERT: F 76 GLU cc_start: 0.6459 (tp30) cc_final: 0.6213 (tp30) REVERT: F 120 ARG cc_start: 0.7340 (ptp-110) cc_final: 0.7068 (ttm-80) REVERT: F 129 VAL cc_start: 0.8138 (t) cc_final: 0.7766 (p) REVERT: F 175 ASP cc_start: 0.8356 (t0) cc_final: 0.7936 (t0) REVERT: F 177 SER cc_start: 0.8790 (m) cc_final: 0.8497 (p) REVERT: F 215 LYS cc_start: 0.8173 (tttt) cc_final: 0.7893 (tttp) REVERT: F 261 LEU cc_start: 0.8507 (tp) cc_final: 0.8286 (mt) REVERT: F 286 LYS cc_start: 0.8288 (tppp) cc_final: 0.8080 (tppp) REVERT: F 290 LYS cc_start: 0.7671 (mttt) cc_final: 0.7392 (mttt) REVERT: H 76 ASN cc_start: 0.6465 (p0) cc_final: 0.5723 (p0) REVERT: L 20 THR cc_start: 0.8609 (t) cc_final: 0.8306 (p) REVERT: L 42 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8028 (mmmt) REVERT: L 90 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6337 (tm130) REVERT: L 104 VAL cc_start: 0.8106 (t) cc_final: 0.7889 (p) outliers start: 72 outliers final: 50 residues processed: 718 average time/residue: 0.1607 time to fit residues: 169.7282 Evaluate side-chains 731 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 674 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 171 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS C 66 GLN C 270 ASN D 288 HIS F 41 HIS F 52 GLN F 288 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103114 restraints weight = 30196.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106051 restraints weight = 12869.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107786 restraints weight = 6716.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108732 restraints weight = 4094.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109446 restraints weight = 2951.046| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19687 Z= 0.237 Angle : 0.669 9.595 26822 Z= 0.348 Chirality : 0.046 0.187 2935 Planarity : 0.004 0.041 3462 Dihedral : 5.602 28.171 2674 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.89 % Favored : 92.02 % Rotamer: Outliers : 4.24 % Allowed : 15.90 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -2.18 (0.16), residues: 2445 helix: -2.34 (0.62), residues: 48 sheet: -0.63 (0.17), residues: 870 loop : -2.01 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 230 TYR 0.022 0.002 TYR A 122 PHE 0.025 0.002 PHE C 356 TRP 0.016 0.002 TRP H 47 HIS 0.017 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00539 (19647) covalent geometry : angle 0.66597 (26742) SS BOND : bond 0.00403 ( 40) SS BOND : angle 1.37003 ( 80) hydrogen bonds : bond 0.03536 ( 493) hydrogen bonds : angle 5.28409 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 685 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7263 (ptm) cc_final: 0.7000 (ptt) REVERT: A 9 SER cc_start: 0.7705 (t) cc_final: 0.7362 (t) REVERT: A 30 SER cc_start: 0.8199 (m) cc_final: 0.7718 (p) REVERT: A 35 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7939 (ttmm) REVERT: A 37 LYS cc_start: 0.8270 (mttt) cc_final: 0.7861 (mtmm) REVERT: A 42 VAL cc_start: 0.8597 (t) cc_final: 0.8102 (m) REVERT: A 45 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6803 (mm-30) REVERT: A 52 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7991 (ttpp) REVERT: A 75 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: A 76 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6340 (tm-30) REVERT: A 105 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7743 (mtpp) REVERT: A 111 SER cc_start: 0.8374 (t) cc_final: 0.7912 (t) REVERT: A 123 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7587 (mtmt) REVERT: A 130 GLN cc_start: 0.7480 (tt0) cc_final: 0.7266 (tt0) REVERT: A 136 THR cc_start: 0.7517 (m) cc_final: 0.7127 (p) REVERT: A 147 TYR cc_start: 0.7782 (m-10) cc_final: 0.7301 (m-10) REVERT: A 176 LYS cc_start: 0.8269 (mttt) cc_final: 0.7964 (mtpp) REVERT: A 205 SER cc_start: 0.8574 (t) cc_final: 0.8083 (p) REVERT: A 218 ASN cc_start: 0.7967 (t0) cc_final: 0.7724 (t0) REVERT: A 241 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6826 (tm-30) REVERT: A 281 ASP cc_start: 0.7758 (t0) cc_final: 0.7450 (t0) REVERT: A 368 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6906 (tm-30) REVERT: B 18 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7598 (ptm-80) REVERT: B 34 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7099 (mm-30) REVERT: B 37 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7158 (mmtt) REVERT: B 44 TYR cc_start: 0.8080 (m-80) cc_final: 0.7480 (m-80) REVERT: B 68 TYR cc_start: 0.8696 (p90) cc_final: 0.8319 (p90) REVERT: B 108 ASP cc_start: 0.7378 (p0) cc_final: 0.7056 (p0) REVERT: B 151 CYS cc_start: 0.6791 (p) cc_final: 0.6030 (p) REVERT: B 164 TYR cc_start: 0.8369 (m-80) cc_final: 0.7850 (m-80) REVERT: B 230 ARG cc_start: 0.8431 (mtp85) cc_final: 0.7936 (ttm110) REVERT: B 254 LYS cc_start: 0.7621 (mmmt) cc_final: 0.6927 (mmmt) REVERT: B 265 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7544 (mmtt) REVERT: B 275 MET cc_start: 0.8023 (mpp) cc_final: 0.7654 (mmm) REVERT: B 290 LYS cc_start: 0.7290 (ttmt) cc_final: 0.7025 (ttmt) REVERT: B 302 ASP cc_start: 0.6725 (p0) cc_final: 0.6497 (p0) REVERT: B 324 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7410 (mtmm) REVERT: B 336 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7864 (ttmm) REVERT: C 10 GLN cc_start: 0.7521 (tt0) cc_final: 0.7120 (tt0) REVERT: C 35 LYS cc_start: 0.8396 (tttt) cc_final: 0.7869 (tttm) REVERT: C 76 GLU cc_start: 0.7631 (tp30) cc_final: 0.6895 (tp30) REVERT: C 105 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7058 (ttmm) REVERT: C 132 PHE cc_start: 0.7585 (m-10) cc_final: 0.7316 (m-10) REVERT: C 184 ILE cc_start: 0.8525 (mm) cc_final: 0.8099 (mt) REVERT: C 186 ASN cc_start: 0.8216 (m-40) cc_final: 0.7954 (m-40) REVERT: C 207 THR cc_start: 0.7984 (t) cc_final: 0.7695 (p) REVERT: C 214 TYR cc_start: 0.8398 (t80) cc_final: 0.7754 (t80) REVERT: C 222 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: C 235 GLN cc_start: 0.8149 (pt0) cc_final: 0.7936 (pt0) REVERT: C 245 LYS cc_start: 0.7796 (mtpt) cc_final: 0.7561 (mtpt) REVERT: C 254 THR cc_start: 0.8473 (p) cc_final: 0.8183 (t) REVERT: C 260 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6754 (mt-10) REVERT: C 261 ILE cc_start: 0.8402 (mm) cc_final: 0.8069 (mm) REVERT: C 269 GLU cc_start: 0.7178 (pt0) cc_final: 0.6682 (pt0) REVERT: C 288 THR cc_start: 0.6782 (OUTLIER) cc_final: 0.6426 (p) REVERT: C 334 SER cc_start: 0.8601 (t) cc_final: 0.8110 (p) REVERT: C 338 THR cc_start: 0.8101 (m) cc_final: 0.7713 (t) REVERT: C 358 THR cc_start: 0.8244 (t) cc_final: 0.8040 (p) REVERT: C 394 HIS cc_start: 0.7476 (p90) cc_final: 0.7144 (p90) REVERT: D 56 ASP cc_start: 0.7800 (p0) cc_final: 0.7534 (p0) REVERT: D 64 ARG cc_start: 0.7335 (mmm-85) cc_final: 0.6999 (mtt-85) REVERT: D 74 ILE cc_start: 0.8244 (mt) cc_final: 0.7905 (mt) REVERT: D 75 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8133 (mttm) REVERT: D 77 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8145 (tt) REVERT: D 88 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7360 (ptt90) REVERT: D 94 ASP cc_start: 0.6911 (t0) cc_final: 0.6665 (t0) REVERT: D 120 ARG cc_start: 0.6836 (tpt-90) cc_final: 0.6487 (tpt-90) REVERT: D 130 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7614 (mtmm) REVERT: D 180 SER cc_start: 0.8207 (p) cc_final: 0.7572 (m) REVERT: D 215 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7468 (ttmm) REVERT: D 257 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8656 (m) REVERT: D 286 LYS cc_start: 0.8025 (tptm) cc_final: 0.7692 (tptm) REVERT: D 316 VAL cc_start: 0.8801 (p) cc_final: 0.8555 (t) REVERT: E 6 THR cc_start: 0.8186 (m) cc_final: 0.7805 (p) REVERT: E 15 TYR cc_start: 0.7308 (t80) cc_final: 0.7071 (t80) REVERT: E 77 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7076 (mt0) REVERT: E 188 ASP cc_start: 0.7050 (t70) cc_final: 0.6663 (t70) REVERT: E 202 ASP cc_start: 0.8201 (p0) cc_final: 0.7904 (p0) REVERT: E 203 ILE cc_start: 0.8134 (mm) cc_final: 0.7661 (tt) REVERT: E 222 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7679 (mt0) REVERT: E 280 PHE cc_start: 0.8412 (m-10) cc_final: 0.7976 (m-10) REVERT: E 324 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7894 (mtmm) REVERT: E 338 THR cc_start: 0.8641 (m) cc_final: 0.8369 (t) REVERT: E 340 LYS cc_start: 0.7751 (tttt) cc_final: 0.7418 (ttmt) REVERT: E 349 GLN cc_start: 0.7146 (tp40) cc_final: 0.6579 (tp40) REVERT: F 8 GLU cc_start: 0.7342 (tp30) cc_final: 0.7029 (tp30) REVERT: F 16 MET cc_start: 0.7970 (mtp) cc_final: 0.7746 (mtp) REVERT: F 19 CYS cc_start: 0.6802 (t) cc_final: 0.6585 (t) REVERT: F 34 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: F 37 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7338 (mmtm) REVERT: F 53 TYR cc_start: 0.8125 (m-80) cc_final: 0.7732 (m-80) REVERT: F 69 ASP cc_start: 0.7323 (t70) cc_final: 0.7047 (t70) REVERT: F 75 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7627 (mmtp) REVERT: F 115 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7432 (mttm) REVERT: F 120 ARG cc_start: 0.7350 (ptp-110) cc_final: 0.7069 (ttm-80) REVERT: F 129 VAL cc_start: 0.8251 (t) cc_final: 0.7910 (p) REVERT: F 175 ASP cc_start: 0.8373 (t0) cc_final: 0.8021 (t0) REVERT: F 177 SER cc_start: 0.8816 (m) cc_final: 0.8483 (p) REVERT: F 215 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7869 (tttp) REVERT: F 261 LEU cc_start: 0.8568 (tp) cc_final: 0.8338 (mt) REVERT: F 290 LYS cc_start: 0.7742 (mttt) cc_final: 0.7460 (mttt) REVERT: H 76 ASN cc_start: 0.6525 (p0) cc_final: 0.5797 (p0) REVERT: L 20 THR cc_start: 0.8591 (t) cc_final: 0.8254 (p) REVERT: L 42 LYS cc_start: 0.8322 (mmmt) cc_final: 0.8074 (mmmt) REVERT: L 58 VAL cc_start: 0.8605 (t) cc_final: 0.8399 (m) REVERT: L 90 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6347 (tm130) REVERT: L 104 VAL cc_start: 0.8246 (t) cc_final: 0.8017 (p) outliers start: 89 outliers final: 61 residues processed: 729 average time/residue: 0.1642 time to fit residues: 175.4684 Evaluate side-chains 750 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 680 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 14 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 170 optimal weight: 0.2980 chunk 195 optimal weight: 0.9990 chunk 227 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 270 ASN E 102 GLN E 349 GLN ** F 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104645 restraints weight = 30357.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107653 restraints weight = 12959.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109432 restraints weight = 6758.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110494 restraints weight = 4115.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111160 restraints weight = 2889.783| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19687 Z= 0.147 Angle : 0.619 8.370 26822 Z= 0.320 Chirality : 0.044 0.172 2935 Planarity : 0.004 0.039 3462 Dihedral : 5.315 26.111 2674 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.33 % Allowed : 16.61 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -2.02 (0.17), residues: 2445 helix: -2.26 (0.63), residues: 48 sheet: -0.56 (0.17), residues: 890 loop : -1.88 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 298 TYR 0.018 0.001 TYR B 238 PHE 0.026 0.001 PHE C 356 TRP 0.014 0.001 TRP D 330 HIS 0.007 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00340 (19647) covalent geometry : angle 0.61608 (26742) SS BOND : bond 0.00263 ( 40) SS BOND : angle 1.24430 ( 80) hydrogen bonds : bond 0.03142 ( 493) hydrogen bonds : angle 5.17197 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 685 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7264 (ptm) cc_final: 0.6977 (ptt) REVERT: A 9 SER cc_start: 0.7666 (t) cc_final: 0.7331 (t) REVERT: A 30 SER cc_start: 0.8160 (m) cc_final: 0.7661 (p) REVERT: A 35 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7700 (ttmm) REVERT: A 37 LYS cc_start: 0.8244 (mttt) cc_final: 0.7784 (mtmm) REVERT: A 42 VAL cc_start: 0.8501 (t) cc_final: 0.7960 (m) REVERT: A 45 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6757 (mm-30) REVERT: A 52 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7996 (ttpp) REVERT: A 75 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: A 76 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6316 (tm-30) REVERT: A 105 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7713 (mtpp) REVERT: A 111 SER cc_start: 0.8367 (t) cc_final: 0.7905 (t) REVERT: A 123 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7434 (mtmt) REVERT: A 136 THR cc_start: 0.7454 (m) cc_final: 0.7037 (p) REVERT: A 147 TYR cc_start: 0.7791 (m-10) cc_final: 0.7457 (m-80) REVERT: A 176 LYS cc_start: 0.8274 (mttt) cc_final: 0.7914 (mtpp) REVERT: A 205 SER cc_start: 0.8527 (t) cc_final: 0.8082 (p) REVERT: A 218 ASN cc_start: 0.7996 (t0) cc_final: 0.7740 (t0) REVERT: A 241 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 269 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6747 (mt-10) REVERT: A 281 ASP cc_start: 0.7737 (t0) cc_final: 0.7361 (t0) REVERT: A 368 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6806 (tm-30) REVERT: B 18 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7639 (ptm-80) REVERT: B 34 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 37 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7097 (mmtt) REVERT: B 44 TYR cc_start: 0.8114 (m-80) cc_final: 0.7455 (m-80) REVERT: B 62 LYS cc_start: 0.7475 (tttt) cc_final: 0.6992 (mtpp) REVERT: B 68 TYR cc_start: 0.8663 (p90) cc_final: 0.8274 (p90) REVERT: B 108 ASP cc_start: 0.7410 (p0) cc_final: 0.7074 (p0) REVERT: B 164 TYR cc_start: 0.8373 (m-80) cc_final: 0.7708 (m-80) REVERT: B 213 LYS cc_start: 0.7996 (mmtm) cc_final: 0.7656 (mmtm) REVERT: B 254 LYS cc_start: 0.7549 (mmmt) cc_final: 0.6850 (mmmt) REVERT: B 275 MET cc_start: 0.8017 (mpp) cc_final: 0.7558 (mmm) REVERT: B 324 LYS cc_start: 0.7660 (mtmm) cc_final: 0.7379 (mtmm) REVERT: B 336 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7784 (ttmm) REVERT: C 10 GLN cc_start: 0.7528 (tt0) cc_final: 0.7220 (tt0) REVERT: C 35 LYS cc_start: 0.8418 (tttt) cc_final: 0.7954 (tttm) REVERT: C 76 GLU cc_start: 0.7652 (tp30) cc_final: 0.6934 (tp30) REVERT: C 105 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7072 (ttmm) REVERT: C 120 GLU cc_start: 0.7649 (pt0) cc_final: 0.7154 (pt0) REVERT: C 125 HIS cc_start: 0.8309 (OUTLIER) cc_final: 0.7919 (p90) REVERT: C 132 PHE cc_start: 0.7569 (m-10) cc_final: 0.7288 (m-10) REVERT: C 178 VAL cc_start: 0.7946 (t) cc_final: 0.7521 (p) REVERT: C 184 ILE cc_start: 0.8488 (mm) cc_final: 0.7932 (mt) REVERT: C 186 ASN cc_start: 0.8208 (m-40) cc_final: 0.7949 (m-40) REVERT: C 207 THR cc_start: 0.7972 (t) cc_final: 0.7685 (p) REVERT: C 214 TYR cc_start: 0.8402 (t80) cc_final: 0.7682 (t80) REVERT: C 222 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7544 (mt0) REVERT: C 242 GLN cc_start: 0.7814 (tp-100) cc_final: 0.7433 (tp-100) REVERT: C 245 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7552 (mtpt) REVERT: C 254 THR cc_start: 0.8425 (p) cc_final: 0.8181 (t) REVERT: C 260 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6651 (mt-10) REVERT: C 261 ILE cc_start: 0.8366 (mm) cc_final: 0.7873 (mm) REVERT: C 266 ILE cc_start: 0.8380 (mt) cc_final: 0.8053 (mm) REVERT: C 288 THR cc_start: 0.6632 (OUTLIER) cc_final: 0.6256 (p) REVERT: C 334 SER cc_start: 0.8589 (t) cc_final: 0.8053 (p) REVERT: C 338 THR cc_start: 0.8091 (m) cc_final: 0.7694 (t) REVERT: C 358 THR cc_start: 0.8224 (t) cc_final: 0.7987 (p) REVERT: C 394 HIS cc_start: 0.7499 (p90) cc_final: 0.7237 (p90) REVERT: D 56 ASP cc_start: 0.7839 (p0) cc_final: 0.7564 (p0) REVERT: D 64 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.6963 (mtt-85) REVERT: D 74 ILE cc_start: 0.8230 (mt) cc_final: 0.7879 (mt) REVERT: D 75 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8130 (mttm) REVERT: D 88 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7383 (ptt90) REVERT: D 94 ASP cc_start: 0.6851 (t0) cc_final: 0.6618 (t0) REVERT: D 130 LYS cc_start: 0.7911 (mtmm) cc_final: 0.7580 (mtmm) REVERT: D 180 SER cc_start: 0.8322 (p) cc_final: 0.7679 (m) REVERT: D 215 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7454 (ttmm) REVERT: D 242 LYS cc_start: 0.8209 (mttm) cc_final: 0.7919 (mttm) REVERT: D 257 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8679 (m) REVERT: D 286 LYS cc_start: 0.8017 (tptm) cc_final: 0.7688 (tptm) REVERT: D 316 VAL cc_start: 0.8757 (p) cc_final: 0.8523 (t) REVERT: D 354 GLU cc_start: 0.5301 (OUTLIER) cc_final: 0.2990 (tp30) REVERT: E 6 THR cc_start: 0.8166 (m) cc_final: 0.7752 (p) REVERT: E 15 TYR cc_start: 0.7339 (t80) cc_final: 0.7107 (t80) REVERT: E 47 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8200 (p) REVERT: E 77 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7062 (mt0) REVERT: E 102 GLN cc_start: 0.8039 (tt0) cc_final: 0.7790 (tt0) REVERT: E 188 ASP cc_start: 0.7042 (t70) cc_final: 0.6668 (t70) REVERT: E 202 ASP cc_start: 0.8178 (p0) cc_final: 0.7951 (p0) REVERT: E 203 ILE cc_start: 0.8110 (mm) cc_final: 0.7856 (pt) REVERT: E 222 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7714 (mt0) REVERT: E 246 ASP cc_start: 0.7046 (m-30) cc_final: 0.6657 (m-30) REVERT: E 280 PHE cc_start: 0.8368 (m-10) cc_final: 0.7920 (m-10) REVERT: E 324 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7874 (mtmm) REVERT: E 338 THR cc_start: 0.8616 (m) cc_final: 0.8291 (t) REVERT: E 340 LYS cc_start: 0.7699 (tttt) cc_final: 0.7388 (ttmt) REVERT: F 8 GLU cc_start: 0.7319 (tp30) cc_final: 0.6992 (tp30) REVERT: F 16 MET cc_start: 0.7968 (mtp) cc_final: 0.7725 (mtp) REVERT: F 19 CYS cc_start: 0.6754 (t) cc_final: 0.6540 (t) REVERT: F 34 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: F 37 LYS cc_start: 0.7610 (mmtt) cc_final: 0.7330 (mmtm) REVERT: F 57 SER cc_start: 0.8432 (p) cc_final: 0.7912 (t) REVERT: F 69 ASP cc_start: 0.7225 (t70) cc_final: 0.6935 (t70) REVERT: F 75 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7312 (mmtp) REVERT: F 76 GLU cc_start: 0.6673 (tp30) cc_final: 0.6292 (mp0) REVERT: F 115 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7453 (mttm) REVERT: F 129 VAL cc_start: 0.8223 (t) cc_final: 0.7825 (p) REVERT: F 175 ASP cc_start: 0.8364 (t0) cc_final: 0.7984 (t0) REVERT: F 177 SER cc_start: 0.8785 (m) cc_final: 0.8455 (p) REVERT: F 215 LYS cc_start: 0.8168 (tttt) cc_final: 0.7824 (tttp) REVERT: F 261 LEU cc_start: 0.8526 (tp) cc_final: 0.8307 (mt) REVERT: F 290 LYS cc_start: 0.7729 (mttt) cc_final: 0.7445 (mttt) REVERT: H 76 ASN cc_start: 0.6411 (p0) cc_final: 0.5684 (p0) REVERT: L 20 THR cc_start: 0.8651 (t) cc_final: 0.8328 (p) REVERT: L 42 LYS cc_start: 0.8305 (mmmt) cc_final: 0.8060 (mmmt) REVERT: L 90 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6369 (tm130) REVERT: L 104 VAL cc_start: 0.8208 (t) cc_final: 0.7972 (p) outliers start: 91 outliers final: 67 residues processed: 729 average time/residue: 0.1641 time to fit residues: 175.3805 Evaluate side-chains 754 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 677 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 11 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 170 optimal weight: 0.0000 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 270 ASN C 157 ASN C 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104030 restraints weight = 30930.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107055 restraints weight = 13355.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108851 restraints weight = 7041.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109929 restraints weight = 4330.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110595 restraints weight = 3068.220| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19687 Z= 0.126 Angle : 0.610 9.961 26822 Z= 0.314 Chirality : 0.044 0.168 2935 Planarity : 0.004 0.038 3462 Dihedral : 5.118 25.431 2674 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.05 % Allowed : 17.33 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -1.91 (0.17), residues: 2445 helix: -2.14 (0.64), residues: 48 sheet: -0.55 (0.17), residues: 903 loop : -1.75 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 21 TYR 0.016 0.001 TYR B 238 PHE 0.026 0.001 PHE C 356 TRP 0.016 0.001 TRP D 330 HIS 0.007 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00292 (19647) covalent geometry : angle 0.60599 (26742) SS BOND : bond 0.00281 ( 40) SS BOND : angle 1.35531 ( 80) hydrogen bonds : bond 0.02996 ( 493) hydrogen bonds : angle 5.08691 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 682 time to evaluate : 0.847 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 7 MET cc_start: 0.7277 (ptm) cc_final: 0.6987 (ptt) REVERT: A 9 SER cc_start: 0.7656 (t) cc_final: 0.7371 (t) REVERT: A 30 SER cc_start: 0.8134 (m) cc_final: 0.7672 (p) REVERT: A 35 LYS cc_start: 0.8442 (ttmt) cc_final: 0.7797 (ttmm) REVERT: A 42 VAL cc_start: 0.8425 (t) cc_final: 0.7868 (m) REVERT: A 45 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6772 (mm-30) REVERT: A 52 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7986 (ttpp) REVERT: A 76 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6344 (tm-30) REVERT: A 79 LYS cc_start: 0.7410 (tttm) cc_final: 0.7196 (tptm) REVERT: A 82 THR cc_start: 0.7668 (m) cc_final: 0.7321 (p) REVERT: A 105 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7722 (mtpp) REVERT: A 111 SER cc_start: 0.8407 (t) cc_final: 0.7963 (t) REVERT: A 123 LYS cc_start: 0.7689 (mtmt) cc_final: 0.7310 (mtmt) REVERT: A 147 TYR cc_start: 0.7819 (m-10) cc_final: 0.7462 (m-80) REVERT: A 176 LYS cc_start: 0.8289 (mttt) cc_final: 0.7927 (mtpp) REVERT: A 205 SER cc_start: 0.8508 (t) cc_final: 0.8080 (p) REVERT: A 218 ASN cc_start: 0.8035 (t0) cc_final: 0.7780 (t0) REVERT: A 241 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6746 (tm-30) REVERT: A 269 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6752 (mt-10) REVERT: A 281 ASP cc_start: 0.7734 (t0) cc_final: 0.7361 (t0) REVERT: A 368 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6738 (tm-30) REVERT: B 18 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7606 (ttt-90) REVERT: B 34 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7132 (mm-30) REVERT: B 37 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7079 (mmtt) REVERT: B 44 TYR cc_start: 0.8099 (m-80) cc_final: 0.7412 (m-80) REVERT: B 62 LYS cc_start: 0.7489 (tttt) cc_final: 0.6987 (mtpp) REVERT: B 68 TYR cc_start: 0.8660 (p90) cc_final: 0.8280 (p90) REVERT: B 108 ASP cc_start: 0.7426 (p0) cc_final: 0.7084 (p0) REVERT: B 137 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6268 (mt-10) REVERT: B 164 TYR cc_start: 0.8313 (m-80) cc_final: 0.7574 (m-80) REVERT: B 213 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7650 (mmtm) REVERT: B 230 ARG cc_start: 0.8307 (mtp85) cc_final: 0.8098 (mtp85) REVERT: B 254 LYS cc_start: 0.7460 (mmmt) cc_final: 0.6797 (mmmt) REVERT: B 275 MET cc_start: 0.8003 (mpp) cc_final: 0.7566 (mmm) REVERT: B 324 LYS cc_start: 0.7642 (mtmm) cc_final: 0.7302 (mtmm) REVERT: B 336 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7782 (ttmm) REVERT: C 10 GLN cc_start: 0.7521 (tt0) cc_final: 0.7239 (tt0) REVERT: C 35 LYS cc_start: 0.8358 (tttt) cc_final: 0.7877 (tttm) REVERT: C 76 GLU cc_start: 0.7636 (tp30) cc_final: 0.6958 (tp30) REVERT: C 105 LYS cc_start: 0.7552 (ttmt) cc_final: 0.7039 (ttmm) REVERT: C 114 CYS cc_start: 0.5620 (t) cc_final: 0.5353 (t) REVERT: C 120 GLU cc_start: 0.7615 (pt0) cc_final: 0.7087 (pt0) REVERT: C 125 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7965 (p90) REVERT: C 132 PHE cc_start: 0.7591 (m-10) cc_final: 0.7299 (m-10) REVERT: C 178 VAL cc_start: 0.8005 (t) cc_final: 0.7554 (p) REVERT: C 184 ILE cc_start: 0.8467 (mm) cc_final: 0.7911 (mt) REVERT: C 207 THR cc_start: 0.7957 (t) cc_final: 0.7663 (p) REVERT: C 214 TYR cc_start: 0.8442 (t80) cc_final: 0.7668 (t80) REVERT: C 222 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: C 235 GLN cc_start: 0.8295 (pt0) cc_final: 0.8074 (pt0) REVERT: C 242 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7406 (tp-100) REVERT: C 245 LYS cc_start: 0.7822 (mtpt) cc_final: 0.7544 (mtpt) REVERT: C 254 THR cc_start: 0.8429 (p) cc_final: 0.8222 (t) REVERT: C 261 ILE cc_start: 0.8367 (mm) cc_final: 0.8047 (mm) REVERT: C 266 ILE cc_start: 0.8387 (mt) cc_final: 0.8063 (mm) REVERT: C 338 THR cc_start: 0.8040 (m) cc_final: 0.7648 (t) REVERT: C 358 THR cc_start: 0.8134 (t) cc_final: 0.7926 (p) REVERT: C 394 HIS cc_start: 0.7498 (p90) cc_final: 0.7277 (p90) REVERT: D 56 ASP cc_start: 0.7779 (p0) cc_final: 0.7532 (p0) REVERT: D 74 ILE cc_start: 0.8197 (mt) cc_final: 0.7879 (mt) REVERT: D 75 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8317 (mmtm) REVERT: D 88 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7407 (ptt90) REVERT: D 94 ASP cc_start: 0.6876 (t0) cc_final: 0.6664 (t0) REVERT: D 120 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6491 (ttt-90) REVERT: D 130 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7618 (mtmm) REVERT: D 147 VAL cc_start: 0.8573 (p) cc_final: 0.8343 (m) REVERT: D 180 SER cc_start: 0.8320 (p) cc_final: 0.7648 (m) REVERT: D 215 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7449 (ttmm) REVERT: D 241 ASP cc_start: 0.7597 (p0) cc_final: 0.7371 (p0) REVERT: D 257 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8669 (m) REVERT: D 277 THR cc_start: 0.8261 (m) cc_final: 0.7830 (p) REVERT: D 286 LYS cc_start: 0.8011 (tptm) cc_final: 0.7670 (tptm) REVERT: D 316 VAL cc_start: 0.8729 (p) cc_final: 0.8494 (t) REVERT: D 354 GLU cc_start: 0.5161 (OUTLIER) cc_final: 0.2846 (tp30) REVERT: E 6 THR cc_start: 0.8177 (m) cc_final: 0.7792 (p) REVERT: E 15 TYR cc_start: 0.7341 (t80) cc_final: 0.7036 (t80) REVERT: E 47 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8232 (p) REVERT: E 77 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7049 (mt0) REVERT: E 188 ASP cc_start: 0.6912 (t70) cc_final: 0.6514 (t70) REVERT: E 202 ASP cc_start: 0.8168 (p0) cc_final: 0.7964 (p0) REVERT: E 203 ILE cc_start: 0.8092 (mm) cc_final: 0.7832 (pt) REVERT: E 222 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7691 (mt0) REVERT: E 280 PHE cc_start: 0.8344 (m-10) cc_final: 0.7946 (m-10) REVERT: E 282 ILE cc_start: 0.8443 (mm) cc_final: 0.8232 (mm) REVERT: E 324 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7875 (mtmm) REVERT: E 338 THR cc_start: 0.8575 (m) cc_final: 0.8261 (t) REVERT: E 340 LYS cc_start: 0.7695 (tttt) cc_final: 0.7372 (ttmt) REVERT: F 16 MET cc_start: 0.7989 (mtp) cc_final: 0.7762 (mtp) REVERT: F 37 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7316 (mmtm) REVERT: F 57 SER cc_start: 0.8462 (p) cc_final: 0.8008 (t) REVERT: F 60 ASN cc_start: 0.7934 (m-40) cc_final: 0.7635 (m-40) REVERT: F 69 ASP cc_start: 0.7144 (t70) cc_final: 0.6887 (t70) REVERT: F 75 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7190 (mmtp) REVERT: F 76 GLU cc_start: 0.6580 (tp30) cc_final: 0.6356 (mp0) REVERT: F 115 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7445 (mttm) REVERT: F 175 ASP cc_start: 0.8390 (t0) cc_final: 0.8027 (t0) REVERT: F 177 SER cc_start: 0.8788 (m) cc_final: 0.8449 (p) REVERT: F 215 LYS cc_start: 0.8157 (tttt) cc_final: 0.7897 (tttp) REVERT: F 261 LEU cc_start: 0.8516 (tp) cc_final: 0.8295 (mt) REVERT: F 290 LYS cc_start: 0.7731 (mttt) cc_final: 0.7433 (mttt) REVERT: H 40 SER cc_start: 0.8290 (p) cc_final: 0.7622 (t) REVERT: H 76 ASN cc_start: 0.6375 (p0) cc_final: 0.5597 (p0) REVERT: L 20 THR cc_start: 0.8624 (t) cc_final: 0.8320 (p) REVERT: L 42 LYS cc_start: 0.8299 (mmmt) cc_final: 0.8046 (mmmt) REVERT: L 90 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6368 (tm130) REVERT: L 104 VAL cc_start: 0.8191 (t) cc_final: 0.7969 (p) outliers start: 85 outliers final: 63 residues processed: 721 average time/residue: 0.1672 time to fit residues: 176.5540 Evaluate side-chains 747 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 676 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 120 optimal weight: 0.0370 chunk 91 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 270 ASN C 66 GLN C 157 ASN E 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103784 restraints weight = 30608.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106805 restraints weight = 13207.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108616 restraints weight = 6971.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109706 restraints weight = 4292.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110376 restraints weight = 3035.438| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19687 Z= 0.140 Angle : 0.623 10.672 26822 Z= 0.320 Chirality : 0.044 0.169 2935 Planarity : 0.004 0.040 3462 Dihedral : 5.104 25.282 2674 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.67 % Favored : 93.29 % Rotamer: Outliers : 3.76 % Allowed : 18.37 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -1.84 (0.17), residues: 2445 helix: -2.09 (0.64), residues: 48 sheet: -0.54 (0.17), residues: 909 loop : -1.68 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 21 TYR 0.034 0.001 TYR F 9 PHE 0.025 0.001 PHE C 356 TRP 0.020 0.002 TRP H 47 HIS 0.007 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00325 (19647) covalent geometry : angle 0.61916 (26742) SS BOND : bond 0.00272 ( 40) SS BOND : angle 1.45841 ( 80) hydrogen bonds : bond 0.03077 ( 493) hydrogen bonds : angle 5.06722 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 670 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7289 (ptm) cc_final: 0.7005 (ptt) REVERT: A 9 SER cc_start: 0.7673 (t) cc_final: 0.7370 (t) REVERT: A 30 SER cc_start: 0.8136 (m) cc_final: 0.7691 (p) REVERT: A 35 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7863 (ttmm) REVERT: A 42 VAL cc_start: 0.8415 (t) cc_final: 0.7870 (m) REVERT: A 45 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 52 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7933 (ttpp) REVERT: A 76 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6333 (tm-30) REVERT: A 79 LYS cc_start: 0.7405 (tttm) cc_final: 0.7203 (tptm) REVERT: A 82 THR cc_start: 0.7635 (m) cc_final: 0.7227 (p) REVERT: A 105 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7719 (mtpp) REVERT: A 111 SER cc_start: 0.8441 (t) cc_final: 0.7982 (t) REVERT: A 123 LYS cc_start: 0.7667 (mtmt) cc_final: 0.7272 (mtmt) REVERT: A 147 TYR cc_start: 0.7807 (m-10) cc_final: 0.7518 (m-10) REVERT: A 176 LYS cc_start: 0.8284 (mttt) cc_final: 0.7933 (mtpp) REVERT: A 205 SER cc_start: 0.8515 (t) cc_final: 0.8089 (p) REVERT: A 218 ASN cc_start: 0.8041 (t0) cc_final: 0.7784 (t0) REVERT: A 241 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6761 (tm-30) REVERT: A 269 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 281 ASP cc_start: 0.7704 (t0) cc_final: 0.7413 (t0) REVERT: A 368 GLN cc_start: 0.7092 (tm-30) cc_final: 0.6723 (tm-30) REVERT: B 18 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7629 (ttt-90) REVERT: B 34 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 37 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7094 (mmtt) REVERT: B 44 TYR cc_start: 0.8092 (m-80) cc_final: 0.7419 (m-80) REVERT: B 62 LYS cc_start: 0.7517 (tttt) cc_final: 0.7019 (mtpp) REVERT: B 68 TYR cc_start: 0.8659 (p90) cc_final: 0.8283 (p90) REVERT: B 108 ASP cc_start: 0.7412 (p0) cc_final: 0.7079 (p0) REVERT: B 164 TYR cc_start: 0.8306 (m-80) cc_final: 0.7576 (m-80) REVERT: B 213 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7642 (mmtm) REVERT: B 254 LYS cc_start: 0.7459 (mmmt) cc_final: 0.6786 (mmmt) REVERT: B 275 MET cc_start: 0.8007 (mpp) cc_final: 0.7566 (mmm) REVERT: B 324 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7310 (mtmm) REVERT: B 336 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7783 (ttmm) REVERT: C 10 GLN cc_start: 0.7521 (tt0) cc_final: 0.7247 (tt0) REVERT: C 35 LYS cc_start: 0.8364 (tttt) cc_final: 0.7902 (tttm) REVERT: C 39 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.7991 (pt) REVERT: C 76 GLU cc_start: 0.7625 (tp30) cc_final: 0.6911 (tp30) REVERT: C 105 LYS cc_start: 0.7506 (ttmt) cc_final: 0.7004 (ttmm) REVERT: C 114 CYS cc_start: 0.5570 (t) cc_final: 0.5260 (t) REVERT: C 120 GLU cc_start: 0.7646 (pt0) cc_final: 0.7130 (pt0) REVERT: C 125 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7958 (p90) REVERT: C 132 PHE cc_start: 0.7583 (m-10) cc_final: 0.7285 (m-10) REVERT: C 184 ILE cc_start: 0.8481 (mm) cc_final: 0.8091 (mt) REVERT: C 207 THR cc_start: 0.7943 (t) cc_final: 0.7644 (p) REVERT: C 214 TYR cc_start: 0.8475 (t80) cc_final: 0.7676 (t80) REVERT: C 222 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: C 254 THR cc_start: 0.8485 (p) cc_final: 0.8220 (t) REVERT: C 266 ILE cc_start: 0.8389 (mt) cc_final: 0.8100 (mm) REVERT: C 288 THR cc_start: 0.6530 (OUTLIER) cc_final: 0.6155 (p) REVERT: C 338 THR cc_start: 0.8030 (m) cc_final: 0.7643 (t) REVERT: D 56 ASP cc_start: 0.7827 (p0) cc_final: 0.7553 (p0) REVERT: D 64 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6914 (mtp85) REVERT: D 74 ILE cc_start: 0.8219 (mt) cc_final: 0.7901 (mt) REVERT: D 75 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8353 (mmtm) REVERT: D 88 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7399 (ptt90) REVERT: D 94 ASP cc_start: 0.6965 (t0) cc_final: 0.6633 (t0) REVERT: D 120 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6477 (ttt-90) REVERT: D 130 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7632 (mtmm) REVERT: D 147 VAL cc_start: 0.8573 (p) cc_final: 0.8347 (m) REVERT: D 180 SER cc_start: 0.8319 (p) cc_final: 0.7746 (m) REVERT: D 215 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7459 (ttmm) REVERT: D 241 ASP cc_start: 0.7681 (p0) cc_final: 0.7454 (p0) REVERT: D 242 LYS cc_start: 0.8143 (mttm) cc_final: 0.7913 (mttm) REVERT: D 257 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8668 (m) REVERT: D 277 THR cc_start: 0.8252 (m) cc_final: 0.7825 (p) REVERT: D 286 LYS cc_start: 0.7998 (tptm) cc_final: 0.7662 (tptm) REVERT: D 316 VAL cc_start: 0.8739 (p) cc_final: 0.8504 (t) REVERT: D 336 LYS cc_start: 0.7790 (mttt) cc_final: 0.7560 (tttt) REVERT: D 354 GLU cc_start: 0.5203 (OUTLIER) cc_final: 0.2790 (tp30) REVERT: E 6 THR cc_start: 0.8174 (m) cc_final: 0.7809 (p) REVERT: E 15 TYR cc_start: 0.7373 (t80) cc_final: 0.7062 (t80) REVERT: E 47 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8264 (p) REVERT: E 77 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7077 (mt0) REVERT: E 188 ASP cc_start: 0.6998 (t70) cc_final: 0.6642 (t70) REVERT: E 202 ASP cc_start: 0.8145 (p0) cc_final: 0.7919 (p0) REVERT: E 203 ILE cc_start: 0.8112 (mm) cc_final: 0.7872 (pt) REVERT: E 222 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7715 (mt0) REVERT: E 246 ASP cc_start: 0.7096 (m-30) cc_final: 0.6794 (m-30) REVERT: E 257 PHE cc_start: 0.8036 (m-80) cc_final: 0.7761 (m-10) REVERT: E 262 TYR cc_start: 0.7458 (m-80) cc_final: 0.6671 (m-80) REVERT: E 280 PHE cc_start: 0.8350 (m-10) cc_final: 0.7957 (m-10) REVERT: E 324 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7919 (mtmm) REVERT: E 338 THR cc_start: 0.8593 (m) cc_final: 0.8270 (t) REVERT: E 340 LYS cc_start: 0.7692 (tttt) cc_final: 0.7374 (ttmt) REVERT: F 16 MET cc_start: 0.7949 (mtp) cc_final: 0.7719 (mtp) REVERT: F 34 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: F 37 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7294 (mmtm) REVERT: F 57 SER cc_start: 0.8433 (p) cc_final: 0.8185 (t) REVERT: F 60 ASN cc_start: 0.8026 (m-40) cc_final: 0.7747 (m-40) REVERT: F 69 ASP cc_start: 0.7160 (t70) cc_final: 0.6852 (t70) REVERT: F 75 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7635 (mmtp) REVERT: F 115 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7450 (mttm) REVERT: F 161 ARG cc_start: 0.7384 (mmm-85) cc_final: 0.7030 (mmm-85) REVERT: F 175 ASP cc_start: 0.8395 (t0) cc_final: 0.8031 (t0) REVERT: F 177 SER cc_start: 0.8768 (m) cc_final: 0.8448 (p) REVERT: F 215 LYS cc_start: 0.8155 (tttt) cc_final: 0.7901 (tttp) REVERT: F 227 ARG cc_start: 0.7493 (mtt-85) cc_final: 0.7167 (mtt90) REVERT: F 261 LEU cc_start: 0.8520 (tp) cc_final: 0.8294 (mt) REVERT: F 286 LYS cc_start: 0.8211 (tppp) cc_final: 0.7971 (ttmm) REVERT: F 290 LYS cc_start: 0.7715 (mttt) cc_final: 0.7423 (mttt) REVERT: F 324 LYS cc_start: 0.8073 (mttt) cc_final: 0.7657 (mttt) REVERT: H 40 SER cc_start: 0.8291 (p) cc_final: 0.7634 (t) REVERT: H 76 ASN cc_start: 0.6339 (p0) cc_final: 0.5580 (p0) REVERT: L 20 THR cc_start: 0.8630 (t) cc_final: 0.8317 (p) REVERT: L 42 LYS cc_start: 0.8281 (mmmt) cc_final: 0.8014 (mmmt) REVERT: L 90 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6368 (tm130) REVERT: L 104 VAL cc_start: 0.8193 (t) cc_final: 0.7979 (p) outliers start: 79 outliers final: 59 residues processed: 709 average time/residue: 0.1697 time to fit residues: 175.3107 Evaluate side-chains 735 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 665 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 238 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 228 optimal weight: 0.0060 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 168 HIS C 235 GLN D 48 GLN E 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104112 restraints weight = 30016.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107096 restraints weight = 12782.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108856 restraints weight = 6669.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109931 restraints weight = 4077.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110584 restraints weight = 2864.703| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19687 Z= 0.190 Angle : 0.662 11.301 26822 Z= 0.341 Chirality : 0.045 0.180 2935 Planarity : 0.004 0.042 3462 Dihedral : 5.282 25.930 2674 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.32 % Favored : 92.64 % Rotamer: Outliers : 3.76 % Allowed : 18.80 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -1.84 (0.17), residues: 2445 helix: -2.11 (0.64), residues: 48 sheet: -0.47 (0.17), residues: 900 loop : -1.74 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 21 TYR 0.032 0.002 TYR F 9 PHE 0.020 0.002 PHE C 356 TRP 0.023 0.002 TRP H 47 HIS 0.010 0.001 HIS C 394 Details of bonding type rmsd covalent geometry : bond 0.00439 (19647) covalent geometry : angle 0.65707 (26742) SS BOND : bond 0.00350 ( 40) SS BOND : angle 1.61048 ( 80) hydrogen bonds : bond 0.03294 ( 493) hydrogen bonds : angle 5.11413 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 672 time to evaluate : 0.718 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 7 MET cc_start: 0.7258 (ptm) cc_final: 0.6988 (ptt) REVERT: A 9 SER cc_start: 0.7689 (t) cc_final: 0.7370 (t) REVERT: A 30 SER cc_start: 0.8153 (m) cc_final: 0.7769 (p) REVERT: A 35 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7873 (ttmm) REVERT: A 42 VAL cc_start: 0.8452 (t) cc_final: 0.7924 (m) REVERT: A 45 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 52 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7798 (ttpp) REVERT: A 76 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 105 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7741 (mtpp) REVERT: A 109 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6912 (ptp) REVERT: A 110 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8490 (mtmm) REVERT: A 111 SER cc_start: 0.8423 (t) cc_final: 0.7975 (t) REVERT: A 123 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7366 (mtmt) REVERT: A 147 TYR cc_start: 0.7813 (m-10) cc_final: 0.7593 (m-10) REVERT: A 176 LYS cc_start: 0.8279 (mttt) cc_final: 0.7930 (mtpp) REVERT: A 205 SER cc_start: 0.8548 (t) cc_final: 0.8080 (p) REVERT: A 218 ASN cc_start: 0.8032 (t0) cc_final: 0.7783 (t0) REVERT: A 241 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6782 (tm-30) REVERT: A 269 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6824 (mt-10) REVERT: A 341 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7091 (mm-30) REVERT: A 368 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 18 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7607 (ttt-90) REVERT: B 34 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7107 (mm-30) REVERT: B 37 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7127 (mmtt) REVERT: B 44 TYR cc_start: 0.8098 (m-80) cc_final: 0.7478 (m-80) REVERT: B 62 LYS cc_start: 0.7615 (tttt) cc_final: 0.7067 (mtpp) REVERT: B 68 TYR cc_start: 0.8668 (p90) cc_final: 0.8286 (p90) REVERT: B 108 ASP cc_start: 0.7392 (p0) cc_final: 0.7083 (p0) REVERT: B 164 TYR cc_start: 0.8354 (m-80) cc_final: 0.7647 (m-80) REVERT: B 254 LYS cc_start: 0.7480 (mmmt) cc_final: 0.6834 (mmmt) REVERT: B 275 MET cc_start: 0.7987 (mpp) cc_final: 0.7547 (mmm) REVERT: B 302 ASP cc_start: 0.6696 (p0) cc_final: 0.6460 (p0) REVERT: B 324 LYS cc_start: 0.7673 (mtmm) cc_final: 0.7318 (mtmm) REVERT: B 336 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7792 (ttmm) REVERT: C 10 GLN cc_start: 0.7523 (tt0) cc_final: 0.7254 (tt0) REVERT: C 35 LYS cc_start: 0.8346 (tttt) cc_final: 0.7864 (tttm) REVERT: C 39 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8010 (pt) REVERT: C 76 GLU cc_start: 0.7597 (tp30) cc_final: 0.6910 (tp30) REVERT: C 105 LYS cc_start: 0.7518 (ttmt) cc_final: 0.6989 (ttmm) REVERT: C 114 CYS cc_start: 0.5548 (t) cc_final: 0.5309 (t) REVERT: C 120 GLU cc_start: 0.7678 (pt0) cc_final: 0.7162 (pt0) REVERT: C 125 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.8082 (p90) REVERT: C 132 PHE cc_start: 0.7571 (m-10) cc_final: 0.7286 (m-10) REVERT: C 184 ILE cc_start: 0.8473 (mm) cc_final: 0.8003 (mt) REVERT: C 207 THR cc_start: 0.7914 (t) cc_final: 0.7612 (p) REVERT: C 214 TYR cc_start: 0.8441 (t80) cc_final: 0.7710 (t80) REVERT: C 222 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: C 235 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7898 (pt0) REVERT: C 254 THR cc_start: 0.8504 (p) cc_final: 0.8262 (t) REVERT: C 266 ILE cc_start: 0.8395 (mt) cc_final: 0.8067 (mm) REVERT: C 288 THR cc_start: 0.6507 (OUTLIER) cc_final: 0.6127 (p) REVERT: C 338 THR cc_start: 0.8057 (m) cc_final: 0.7672 (t) REVERT: D 56 ASP cc_start: 0.7790 (p0) cc_final: 0.7528 (p0) REVERT: D 64 ARG cc_start: 0.7281 (mmm-85) cc_final: 0.6900 (mtp85) REVERT: D 74 ILE cc_start: 0.8242 (mt) cc_final: 0.7947 (mt) REVERT: D 88 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7397 (ptt90) REVERT: D 120 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6443 (ttt-90) REVERT: D 130 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7708 (mtmm) REVERT: D 147 VAL cc_start: 0.8573 (p) cc_final: 0.8346 (m) REVERT: D 180 SER cc_start: 0.8408 (p) cc_final: 0.7885 (m) REVERT: D 215 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7479 (ttmm) REVERT: D 257 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8626 (m) REVERT: D 277 THR cc_start: 0.8264 (m) cc_final: 0.7811 (p) REVERT: D 286 LYS cc_start: 0.8003 (tptm) cc_final: 0.7660 (tptm) REVERT: D 316 VAL cc_start: 0.8778 (p) cc_final: 0.8518 (t) REVERT: D 336 LYS cc_start: 0.7790 (mttt) cc_final: 0.7566 (tttt) REVERT: D 354 GLU cc_start: 0.5384 (OUTLIER) cc_final: 0.2777 (tp30) REVERT: E 6 THR cc_start: 0.8183 (m) cc_final: 0.7823 (p) REVERT: E 15 TYR cc_start: 0.7368 (t80) cc_final: 0.7049 (t80) REVERT: E 77 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7094 (mt0) REVERT: E 99 GLU cc_start: 0.7129 (tt0) cc_final: 0.6904 (tt0) REVERT: E 188 ASP cc_start: 0.7003 (t70) cc_final: 0.6649 (t70) REVERT: E 202 ASP cc_start: 0.8171 (p0) cc_final: 0.7951 (p0) REVERT: E 203 ILE cc_start: 0.8110 (mm) cc_final: 0.7870 (pt) REVERT: E 222 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7687 (mt0) REVERT: E 246 ASP cc_start: 0.7085 (m-30) cc_final: 0.6770 (m-30) REVERT: E 257 PHE cc_start: 0.8031 (m-80) cc_final: 0.7764 (m-10) REVERT: E 280 PHE cc_start: 0.8407 (m-10) cc_final: 0.7954 (m-10) REVERT: E 324 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7913 (mtmm) REVERT: E 338 THR cc_start: 0.8638 (m) cc_final: 0.8309 (t) REVERT: E 340 LYS cc_start: 0.7700 (tttt) cc_final: 0.7379 (ttmt) REVERT: F 16 MET cc_start: 0.7993 (mtp) cc_final: 0.7773 (mtp) REVERT: F 34 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: F 37 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7333 (mmtm) REVERT: F 57 SER cc_start: 0.8344 (p) cc_final: 0.8112 (m) REVERT: F 60 ASN cc_start: 0.7966 (m-40) cc_final: 0.7718 (m-40) REVERT: F 69 ASP cc_start: 0.7085 (t70) cc_final: 0.6861 (t70) REVERT: F 75 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7813 (mmtp) REVERT: F 115 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7492 (mttm) REVERT: F 129 VAL cc_start: 0.8202 (t) cc_final: 0.7866 (p) REVERT: F 161 ARG cc_start: 0.7396 (mmm-85) cc_final: 0.7048 (mmm-85) REVERT: F 177 SER cc_start: 0.8788 (m) cc_final: 0.8413 (p) REVERT: F 215 LYS cc_start: 0.8201 (tttt) cc_final: 0.7842 (tttp) REVERT: F 261 LEU cc_start: 0.8525 (tp) cc_final: 0.8304 (mt) REVERT: F 286 LYS cc_start: 0.8260 (tppp) cc_final: 0.8032 (ttmm) REVERT: F 290 LYS cc_start: 0.7727 (mttt) cc_final: 0.7439 (mttt) REVERT: F 322 THR cc_start: 0.8324 (p) cc_final: 0.8123 (m) REVERT: F 324 LYS cc_start: 0.8084 (mttt) cc_final: 0.7687 (mttt) REVERT: H 40 SER cc_start: 0.8326 (p) cc_final: 0.7660 (t) REVERT: H 76 ASN cc_start: 0.6404 (p0) cc_final: 0.5640 (p0) REVERT: L 20 THR cc_start: 0.8657 (t) cc_final: 0.8329 (p) REVERT: L 42 LYS cc_start: 0.8300 (mmmt) cc_final: 0.8045 (mmmt) REVERT: L 60 SER cc_start: 0.8581 (p) cc_final: 0.8317 (t) REVERT: L 90 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6370 (tm130) REVERT: L 104 VAL cc_start: 0.8276 (t) cc_final: 0.8058 (p) outliers start: 79 outliers final: 64 residues processed: 712 average time/residue: 0.1697 time to fit residues: 176.6293 Evaluate side-chains 752 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 676 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 147 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 270 ASN C 235 GLN ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103879 restraints weight = 30182.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106868 restraints weight = 12820.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108637 restraints weight = 6671.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109716 restraints weight = 4052.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110377 restraints weight = 2838.111| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 19687 Z= 0.316 Angle : 0.969 59.200 26822 Z= 0.588 Chirality : 0.057 1.354 2935 Planarity : 0.005 0.150 3462 Dihedral : 5.303 25.811 2674 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.32 % Favored : 92.64 % Rotamer: Outliers : 3.90 % Allowed : 18.61 % Favored : 77.49 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % 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: -1.84 (0.17), residues: 2445 helix: -2.15 (0.63), residues: 48 sheet: -0.45 (0.17), residues: 893 loop : -1.75 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 206 TYR 0.036 0.002 TYR F 9 PHE 0.022 0.002 PHE C 356 TRP 0.022 0.002 TRP H 47 HIS 0.142 0.002 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00664 (19647) covalent geometry : angle 0.96654 (26742) SS BOND : bond 0.00423 ( 40) SS BOND : angle 1.61567 ( 80) hydrogen bonds : bond 0.03390 ( 493) hydrogen bonds : angle 5.11810 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4097.29 seconds wall clock time: 71 minutes 23.82 seconds (4283.82 seconds total)