Starting phenix.real_space_refine on Mon Jun 16 19:30:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eeu_28058/06_2025/8eeu_28058.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eeu_28058/06_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_28058/06_2025/8eeu_28058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eeu_28058/06_2025/8eeu_28058.map" model { file = "/net/cci-nas-00/data/ceres_data/8eeu_28058/06_2025/8eeu_28058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eeu_28058/06_2025/8eeu_28058.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.80, per 1000 atoms: 0.62 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: 4.29 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.82 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: 6.24 Time building geometry restraints manager: 5.09 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.770 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.003 TRP D 236 HIS 0.018 0.003 HIS D 168 PHE 0.030 0.003 PHE F 328 TYR 0.038 0.003 TYR F 9 ARG 0.014 0.002 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.15821 ( 493) hydrogen bonds : angle 8.35173 ( 1251) SS BOND : bond 0.00610 ( 40) SS BOND : angle 1.89068 ( 80) covalent geometry : bond 0.01156 (19647) covalent geometry : angle 0.93528 (26742) *********************** 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 : 1.987 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: 0.3567 time to fit residues: 429.2024 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 : 2.014 ------------------------------------------------------------------------------- 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 205 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 190 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 220 optimal weight: 0.3980 overall best weight: 0.5520 ------------------------------------------------------------------------------- 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 130 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN C 222 GLN D 71 HIS D 288 HIS E 157 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111030 restraints weight = 30077.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113981 restraints weight = 12705.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115718 restraints weight = 6568.433| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19687 Z= 0.132 Angle : 0.640 8.574 26822 Z= 0.335 Chirality : 0.046 0.201 2935 Planarity : 0.006 0.048 3462 Dihedral : 5.858 29.960 2676 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.75 % Favored : 93.21 % Rotamer: Outliers : 1.48 % Allowed : 8.81 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.15), residues: 2445 helix: -3.47 (0.45), residues: 54 sheet: -1.86 (0.15), residues: 944 loop : -2.81 (0.14), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 236 HIS 0.007 0.001 HIS C 394 PHE 0.020 0.002 PHE C 287 TYR 0.025 0.001 TYR A 122 ARG 0.005 0.001 ARG D 21 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 493) hydrogen bonds : angle 5.96238 ( 1251) SS BOND : bond 0.00256 ( 40) SS BOND : angle 1.13535 ( 80) covalent geometry : bond 0.00302 (19647) covalent geometry : angle 0.63750 (26742) *********************** 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 767 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 736 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7659 (t) cc_final: 0.7368 (t) REVERT: A 29 ILE cc_start: 0.8597 (mt) cc_final: 0.8396 (mp) REVERT: A 30 SER cc_start: 0.8323 (m) cc_final: 0.7674 (p) REVERT: A 35 LYS cc_start: 0.8375 (ttmt) cc_final: 0.7602 (ttmm) REVERT: A 37 LYS cc_start: 0.8226 (mttt) cc_final: 0.8006 (mtmm) REVERT: A 42 VAL cc_start: 0.8301 (t) cc_final: 0.7812 (m) REVERT: A 45 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6759 (mm-30) REVERT: A 52 LYS cc_start: 0.8312 (ttpt) cc_final: 0.7966 (ttpp) REVERT: A 76 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6161 (tm-30) REVERT: A 82 THR cc_start: 0.7583 (m) cc_final: 0.7353 (p) REVERT: A 105 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7784 (mtpp) REVERT: A 111 SER cc_start: 0.7920 (t) cc_final: 0.7302 (t) REVERT: A 123 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7371 (mtmt) REVERT: A 130 GLN cc_start: 0.7493 (tt0) cc_final: 0.7161 (tt0) REVERT: A 137 VAL cc_start: 0.8118 (t) cc_final: 0.7723 (p) REVERT: A 147 TYR cc_start: 0.7629 (m-10) cc_final: 0.7212 (m-80) REVERT: A 176 LYS cc_start: 0.8170 (mttt) cc_final: 0.7816 (mtpp) REVERT: A 205 SER cc_start: 0.8566 (t) cc_final: 0.8139 (p) REVERT: A 252 LYS cc_start: 0.8712 (tttt) cc_final: 0.8477 (ttmm) REVERT: A 269 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6614 (mt-10) REVERT: A 281 ASP cc_start: 0.7778 (t0) cc_final: 0.7469 (t0) REVERT: A 284 ASP cc_start: 0.6997 (m-30) cc_final: 0.6746 (m-30) REVERT: A 291 SER cc_start: 0.8265 (p) cc_final: 0.8038 (t) REVERT: A 300 GLU cc_start: 0.7196 (pt0) cc_final: 0.6905 (pt0) REVERT: A 307 VAL cc_start: 0.8755 (t) cc_final: 0.8483 (p) REVERT: A 339 LEU cc_start: 0.8632 (mp) cc_final: 0.8424 (mt) REVERT: A 341 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 345 GLU cc_start: 0.7403 (mp0) cc_final: 0.7197 (mp0) REVERT: A 368 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6870 (tm-30) REVERT: A 377 LYS cc_start: 0.7704 (mttp) cc_final: 0.7496 (mttp) REVERT: B 34 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7045 (mm-30) REVERT: B 37 LYS cc_start: 0.7559 (mmtt) cc_final: 0.7164 (mttt) REVERT: B 68 TYR cc_start: 0.8663 (p90) cc_final: 0.8415 (p90) REVERT: B 108 ASP cc_start: 0.7400 (p0) cc_final: 0.7000 (p0) REVERT: B 115 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7241 (mtpp) REVERT: B 164 TYR cc_start: 0.8047 (m-80) cc_final: 0.7491 (m-80) REVERT: B 175 ASP cc_start: 0.6782 (t0) cc_final: 0.6517 (t0) REVERT: B 192 ASP cc_start: 0.7073 (t70) cc_final: 0.6852 (t70) REVERT: B 236 TRP cc_start: 0.8738 (m-10) cc_final: 0.8507 (m-10) REVERT: B 294 TYR cc_start: 0.7612 (m-10) cc_final: 0.7192 (m-80) REVERT: B 324 LYS cc_start: 0.7591 (mtmm) cc_final: 0.7325 (mtmm) REVERT: B 336 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7856 (ttmm) REVERT: C 26 PRO cc_start: 0.7836 (Cg_exo) cc_final: 0.7619 (Cg_endo) REVERT: C 104 SER cc_start: 0.7961 (m) cc_final: 0.7752 (t) REVERT: C 117 ASP cc_start: 0.7594 (t70) cc_final: 0.7296 (t70) REVERT: C 120 GLU cc_start: 0.7621 (pt0) cc_final: 0.7207 (pt0) REVERT: C 186 ASN cc_start: 0.8036 (m110) cc_final: 0.7712 (m110) REVERT: C 245 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7431 (mtpt) REVERT: C 246 ASP cc_start: 0.6851 (m-30) cc_final: 0.6552 (m-30) REVERT: C 254 THR cc_start: 0.8406 (p) cc_final: 0.8129 (t) REVERT: C 261 ILE cc_start: 0.8098 (mm) cc_final: 0.7697 (mm) REVERT: C 334 SER cc_start: 0.8563 (t) cc_final: 0.8124 (p) REVERT: C 392 GLN cc_start: 0.7781 (mt0) cc_final: 0.7533 (mt0) REVERT: D 31 ILE cc_start: 0.8024 (tt) cc_final: 0.7720 (tt) REVERT: D 64 ARG cc_start: 0.7179 (mmm-85) cc_final: 0.6780 (mtt-85) REVERT: D 74 ILE cc_start: 0.8197 (mt) cc_final: 0.7942 (mt) REVERT: D 75 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8158 (mttm) REVERT: D 77 ILE cc_start: 0.8358 (mt) cc_final: 0.7957 (tt) REVERT: D 82 VAL cc_start: 0.8664 (t) cc_final: 0.8383 (p) REVERT: D 94 ASP cc_start: 0.6919 (t0) cc_final: 0.6671 (t0) REVERT: D 122 SER cc_start: 0.8467 (t) cc_final: 0.8208 (m) REVERT: D 130 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7414 (mtmm) REVERT: D 134 VAL cc_start: 0.8562 (t) cc_final: 0.8306 (t) REVERT: D 176 SER cc_start: 0.7864 (p) cc_final: 0.7582 (t) REVERT: D 180 SER cc_start: 0.7891 (p) cc_final: 0.7472 (m) REVERT: D 215 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7571 (ttmm) REVERT: D 254 LYS cc_start: 0.8498 (mtmp) cc_final: 0.8186 (mtpp) REVERT: D 338 PHE cc_start: 0.8147 (m-10) cc_final: 0.7829 (m-80) REVERT: E 6 THR cc_start: 0.8059 (m) cc_final: 0.7663 (p) REVERT: E 9 SER cc_start: 0.8430 (t) cc_final: 0.8140 (t) REVERT: E 15 TYR cc_start: 0.7262 (t80) cc_final: 0.6970 (t80) REVERT: E 47 VAL cc_start: 0.8347 (m) cc_final: 0.8004 (p) REVERT: E 79 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7673 (ttmm) REVERT: E 157 ASN cc_start: 0.7694 (t0) cc_final: 0.7462 (t0) REVERT: E 188 ASP cc_start: 0.6972 (t70) cc_final: 0.6593 (t70) REVERT: E 202 ASP cc_start: 0.7970 (p0) cc_final: 0.7729 (p0) REVERT: E 222 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7603 (mt0) REVERT: E 246 ASP cc_start: 0.7124 (m-30) cc_final: 0.6767 (m-30) REVERT: E 252 LYS cc_start: 0.8022 (tttt) cc_final: 0.7768 (ptmm) REVERT: E 260 GLU cc_start: 0.6454 (mt-10) cc_final: 0.6235 (mt-10) REVERT: E 262 TYR cc_start: 0.7608 (m-80) cc_final: 0.6049 (m-80) REVERT: E 269 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7135 (mt-10) REVERT: E 300 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6921 (tm-30) REVERT: E 304 ASN cc_start: 0.7974 (m110) cc_final: 0.7579 (m-40) REVERT: E 324 LYS cc_start: 0.8256 (mtmp) cc_final: 0.8005 (mtmm) REVERT: E 338 THR cc_start: 0.8347 (m) cc_final: 0.8097 (t) REVERT: E 340 LYS cc_start: 0.7568 (tttt) cc_final: 0.7287 (ttmt) REVERT: F 8 GLU cc_start: 0.7388 (tp30) cc_final: 0.7096 (tp30) REVERT: F 12 THR cc_start: 0.8012 (m) cc_final: 0.7602 (t) REVERT: F 37 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7182 (mmtm) REVERT: F 53 TYR cc_start: 0.8219 (m-80) cc_final: 0.7745 (m-80) REVERT: F 57 SER cc_start: 0.8401 (p) cc_final: 0.8173 (t) REVERT: F 60 ASN cc_start: 0.7940 (m-40) cc_final: 0.7625 (m-40) REVERT: F 75 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7866 (mmtp) REVERT: F 100 LEU cc_start: 0.8094 (tp) cc_final: 0.7890 (tt) REVERT: F 175 ASP cc_start: 0.8189 (t0) cc_final: 0.7789 (t0) REVERT: F 177 SER cc_start: 0.8725 (m) cc_final: 0.8411 (p) REVERT: F 215 LYS cc_start: 0.7996 (tttt) cc_final: 0.7560 (tttp) REVERT: F 254 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7716 (mtmt) REVERT: F 290 LYS cc_start: 0.7484 (mttt) cc_final: 0.7255 (mttt) REVERT: F 347 ASN cc_start: 0.8323 (t0) cc_final: 0.8033 (t0) REVERT: H 39 GLN cc_start: 0.8313 (tt0) cc_final: 0.7926 (tt0) REVERT: H 85 GLU cc_start: 0.7953 (tp30) cc_final: 0.7638 (tp30) REVERT: L 20 THR cc_start: 0.8627 (t) cc_final: 0.8325 (p) REVERT: L 42 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7953 (mmmt) REVERT: L 104 VAL cc_start: 0.7989 (t) cc_final: 0.7661 (p) outliers start: 31 outliers final: 20 residues processed: 752 average time/residue: 0.4077 time to fit residues: 452.1201 Evaluate side-chains 723 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 703 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 THR Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 110 ILE 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 E residue 334 SER Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 64 optimal weight: 0.0040 chunk 57 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 102 GLN A 179 GLN A 235 GLN A 270 ASN B 288 HIS B 333 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS D 71 HIS E 125 HIS E 360 ASN E 362 HIS F 52 GLN F 81 GLN F 132 ASN F 305 HIS F 318 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104496 restraints weight = 30764.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107526 restraints weight = 13330.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109318 restraints weight = 7030.245| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19687 Z= 0.196 Angle : 0.645 8.002 26822 Z= 0.337 Chirality : 0.046 0.161 2935 Planarity : 0.005 0.046 3462 Dihedral : 5.680 28.760 2674 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.69 % Favored : 92.23 % Rotamer: Outliers : 2.90 % Allowed : 12.38 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.16), residues: 2445 helix: -2.69 (0.57), residues: 48 sheet: -1.32 (0.16), residues: 930 loop : -2.42 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 103 HIS 0.006 0.001 HIS C 394 PHE 0.023 0.002 PHE C 356 TYR 0.050 0.002 TYR F 9 ARG 0.006 0.001 ARG E 73 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 493) hydrogen bonds : angle 5.53312 ( 1251) SS BOND : bond 0.00418 ( 40) SS BOND : angle 1.20716 ( 80) covalent geometry : bond 0.00445 (19647) covalent geometry : angle 0.64266 (26742) *********************** 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 781 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 720 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7700 (t) cc_final: 0.7376 (t) REVERT: A 18 ILE cc_start: 0.8267 (pt) cc_final: 0.7990 (mm) REVERT: A 30 SER cc_start: 0.8267 (m) cc_final: 0.7759 (p) REVERT: A 35 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7493 (ttmm) REVERT: A 37 LYS cc_start: 0.8263 (mttt) cc_final: 0.7706 (mtmm) REVERT: A 42 VAL cc_start: 0.8589 (t) cc_final: 0.8096 (m) REVERT: A 45 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6881 (mm-30) REVERT: A 52 LYS cc_start: 0.8376 (ttpt) cc_final: 0.8057 (ttpp) REVERT: A 56 ASP cc_start: 0.6647 (t0) cc_final: 0.6395 (t0) REVERT: A 75 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: A 76 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6214 (tm-30) REVERT: A 105 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7778 (mtpp) REVERT: A 111 SER cc_start: 0.8144 (t) cc_final: 0.7728 (t) REVERT: A 123 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7473 (mtmt) REVERT: A 130 GLN cc_start: 0.7501 (tt0) cc_final: 0.7275 (tt0) REVERT: A 147 TYR cc_start: 0.7696 (m-10) cc_final: 0.7232 (m-10) REVERT: A 176 LYS cc_start: 0.8256 (mttt) cc_final: 0.7950 (mtpp) REVERT: A 205 SER cc_start: 0.8526 (t) cc_final: 0.8127 (p) REVERT: A 241 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 252 LYS cc_start: 0.8758 (tttt) cc_final: 0.8504 (ttmm) REVERT: A 269 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6509 (mt-10) REVERT: A 281 ASP cc_start: 0.7813 (t0) cc_final: 0.7523 (t0) REVERT: A 307 VAL cc_start: 0.8747 (t) cc_final: 0.8496 (p) REVERT: A 344 VAL cc_start: 0.8411 (m) cc_final: 0.8087 (p) REVERT: A 368 GLN cc_start: 0.7194 (tm-30) cc_final: 0.6933 (tm-30) REVERT: B 34 GLU cc_start: 0.7284 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 37 LYS cc_start: 0.7679 (mmtt) cc_final: 0.7202 (mmtt) REVERT: B 62 LYS cc_start: 0.7363 (tttt) cc_final: 0.6841 (mtpp) REVERT: B 68 TYR cc_start: 0.8665 (p90) cc_final: 0.8342 (p90) REVERT: B 108 ASP cc_start: 0.7433 (p0) cc_final: 0.7027 (p0) REVERT: B 115 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7291 (mtpp) REVERT: B 148 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 159 GLN cc_start: 0.7944 (mt0) cc_final: 0.7624 (mt0) REVERT: B 164 TYR cc_start: 0.8141 (m-80) cc_final: 0.7498 (m-80) REVERT: B 230 ARG cc_start: 0.8459 (mtp85) cc_final: 0.7972 (ttm110) REVERT: B 254 LYS cc_start: 0.7529 (mmmt) cc_final: 0.7277 (mmmt) REVERT: B 265 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7387 (mmmm) REVERT: B 294 TYR cc_start: 0.8017 (m-10) cc_final: 0.7595 (m-80) REVERT: B 324 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7396 (mtmm) REVERT: B 336 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7899 (ttmm) REVERT: C 10 GLN cc_start: 0.7595 (tt0) cc_final: 0.7370 (tt0) REVERT: C 37 LYS cc_start: 0.7599 (ttmt) cc_final: 0.7332 (ttmm) REVERT: C 159 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7596 (p) REVERT: C 186 ASN cc_start: 0.8184 (m110) cc_final: 0.7868 (m110) REVERT: C 207 THR cc_start: 0.7992 (t) cc_final: 0.7711 (p) REVERT: C 216 ASN cc_start: 0.7856 (t0) cc_final: 0.7604 (t0) REVERT: C 242 GLN cc_start: 0.7645 (tp40) cc_final: 0.7193 (tp-100) REVERT: C 245 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7531 (mtpt) REVERT: C 246 ASP cc_start: 0.6852 (m-30) cc_final: 0.6559 (m-30) REVERT: C 254 THR cc_start: 0.8520 (p) cc_final: 0.8221 (t) REVERT: C 260 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6669 (mt-10) REVERT: C 261 ILE cc_start: 0.8304 (mm) cc_final: 0.7908 (mm) REVERT: C 334 SER cc_start: 0.8563 (t) cc_final: 0.8102 (p) REVERT: C 362 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.7093 (m170) REVERT: C 379 ASP cc_start: 0.6991 (t0) cc_final: 0.6767 (t0) REVERT: D 64 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.6847 (mtt-85) REVERT: D 66 MET cc_start: 0.8258 (ttm) cc_final: 0.8005 (ttp) REVERT: D 74 ILE cc_start: 0.8212 (mt) cc_final: 0.7974 (mt) REVERT: D 75 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8118 (mttm) REVERT: D 77 ILE cc_start: 0.8456 (mt) cc_final: 0.8101 (tt) REVERT: D 94 ASP cc_start: 0.6860 (t0) cc_final: 0.6591 (t0) REVERT: D 120 ARG cc_start: 0.6799 (tpt-90) cc_final: 0.6556 (tpt-90) REVERT: D 130 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7430 (mtmm) REVERT: D 134 VAL cc_start: 0.8600 (t) cc_final: 0.8359 (t) REVERT: D 180 SER cc_start: 0.8059 (p) cc_final: 0.7641 (m) REVERT: D 215 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7543 (ttmm) REVERT: D 241 ASP cc_start: 0.7749 (p0) cc_final: 0.7473 (p0) REVERT: D 242 LYS cc_start: 0.8074 (mttm) cc_final: 0.7820 (mttp) REVERT: D 254 LYS cc_start: 0.8591 (mtmp) cc_final: 0.8185 (mtpp) REVERT: D 316 VAL cc_start: 0.8747 (t) cc_final: 0.8476 (p) REVERT: D 338 PHE cc_start: 0.8134 (m-10) cc_final: 0.7880 (m-80) REVERT: E 6 THR cc_start: 0.8159 (m) cc_final: 0.7758 (p) REVERT: E 15 TYR cc_start: 0.7332 (t80) cc_final: 0.7061 (t80) REVERT: E 47 VAL cc_start: 0.8331 (m) cc_final: 0.8035 (p) REVERT: E 110 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8164 (mtmm) REVERT: E 157 ASN cc_start: 0.7749 (t0) cc_final: 0.7432 (t0) REVERT: E 188 ASP cc_start: 0.7011 (t70) cc_final: 0.6606 (t70) REVERT: E 202 ASP cc_start: 0.8162 (p0) cc_final: 0.7902 (p0) REVERT: E 222 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7667 (mt0) REVERT: E 246 ASP cc_start: 0.7144 (m-30) cc_final: 0.6808 (m-30) REVERT: E 252 LYS cc_start: 0.8121 (tttt) cc_final: 0.7905 (tttt) REVERT: E 269 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7115 (mt-10) REVERT: E 280 PHE cc_start: 0.8440 (m-10) cc_final: 0.8066 (m-10) REVERT: E 300 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6884 (tm-30) REVERT: E 304 ASN cc_start: 0.8011 (m110) cc_final: 0.7684 (m-40) REVERT: E 324 LYS cc_start: 0.8256 (mtmp) cc_final: 0.8043 (mtmm) REVERT: E 338 THR cc_start: 0.8523 (m) cc_final: 0.8264 (t) REVERT: E 340 LYS cc_start: 0.7716 (tttt) cc_final: 0.7399 (ttmt) REVERT: E 377 LYS cc_start: 0.6827 (mtpm) cc_final: 0.6544 (mtpm) REVERT: F 8 GLU cc_start: 0.7396 (tp30) cc_final: 0.7098 (tp30) REVERT: F 16 MET cc_start: 0.7925 (mtp) cc_final: 0.7702 (mtp) REVERT: F 19 CYS cc_start: 0.6808 (t) cc_final: 0.6556 (t) REVERT: F 53 TYR cc_start: 0.8153 (m-80) cc_final: 0.7703 (m-80) REVERT: F 57 SER cc_start: 0.8453 (p) cc_final: 0.7955 (t) REVERT: F 60 ASN cc_start: 0.8081 (m-40) cc_final: 0.7741 (m-40) REVERT: F 69 ASP cc_start: 0.7504 (t70) cc_final: 0.7201 (t70) REVERT: F 75 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7468 (mmtp) REVERT: F 76 GLU cc_start: 0.6601 (tp30) cc_final: 0.6173 (tp30) REVERT: F 129 VAL cc_start: 0.8188 (t) cc_final: 0.7857 (p) REVERT: F 175 ASP cc_start: 0.8314 (t0) cc_final: 0.7865 (t0) REVERT: F 177 SER cc_start: 0.8723 (m) cc_final: 0.8450 (p) REVERT: F 241 ASP cc_start: 0.7656 (p0) cc_final: 0.7434 (p0) REVERT: F 245 LYS cc_start: 0.8220 (ptmt) cc_final: 0.7890 (ptmt) REVERT: F 261 LEU cc_start: 0.8544 (tp) cc_final: 0.8289 (mt) REVERT: F 290 LYS cc_start: 0.7692 (mttt) cc_final: 0.7410 (mttt) REVERT: F 347 ASN cc_start: 0.8462 (t0) cc_final: 0.8168 (t0) REVERT: H 38 ARG cc_start: 0.7122 (ptt-90) cc_final: 0.6852 (ptt-90) REVERT: H 76 ASN cc_start: 0.6437 (p0) cc_final: 0.5791 (p0) REVERT: L 20 THR cc_start: 0.8662 (t) cc_final: 0.8346 (p) REVERT: L 42 LYS cc_start: 0.8278 (mmmt) cc_final: 0.8030 (mmmt) REVERT: L 54 LEU cc_start: 0.8720 (tp) cc_final: 0.8410 (tp) REVERT: L 104 VAL cc_start: 0.8065 (t) cc_final: 0.7838 (p) outliers start: 61 outliers final: 40 residues processed: 744 average time/residue: 0.4044 time to fit residues: 444.6495 Evaluate side-chains 728 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 685 time to evaluate : 2.596 ------------------------------------------------------------------------------- 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 167 MET 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 55 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 220 VAL 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 318 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 147 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 242 optimal weight: 0.5980 chunk 190 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 218 ASN A 242 GLN A 270 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 362 HIS F 52 GLN F 81 GLN F 132 ASN F 305 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106752 restraints weight = 30915.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109738 restraints weight = 13238.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111486 restraints weight = 6900.432| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3213 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= 0.109 Angle : 0.595 8.236 26822 Z= 0.307 Chirality : 0.044 0.167 2935 Planarity : 0.004 0.042 3462 Dihedral : 5.245 26.554 2674 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.58 % Favored : 93.37 % Rotamer: Outliers : 3.00 % Allowed : 14.66 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.16), residues: 2445 helix: -2.01 (0.66), residues: 48 sheet: -1.08 (0.17), residues: 946 loop : -2.13 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 236 HIS 0.009 0.001 HIS C 362 PHE 0.036 0.001 PHE E 257 TYR 0.044 0.001 TYR F 9 ARG 0.006 0.000 ARG D 227 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 493) hydrogen bonds : angle 5.22301 ( 1251) SS BOND : bond 0.00232 ( 40) SS BOND : angle 1.17557 ( 80) covalent geometry : bond 0.00251 (19647) covalent geometry : angle 0.59230 (26742) *********************** 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 750 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 687 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7634 (t) cc_final: 0.7333 (t) REVERT: A 18 ILE cc_start: 0.8042 (pt) cc_final: 0.7788 (mm) REVERT: A 30 SER cc_start: 0.8169 (m) cc_final: 0.7679 (p) REVERT: A 35 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7676 (ttmm) REVERT: A 42 VAL cc_start: 0.8441 (t) cc_final: 0.7905 (m) REVERT: A 45 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 52 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8128 (ttpp) REVERT: A 76 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6283 (tm-30) REVERT: A 82 THR cc_start: 0.7631 (m) cc_final: 0.7333 (p) REVERT: A 105 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7724 (mtpp) REVERT: A 111 SER cc_start: 0.8141 (t) cc_final: 0.7731 (t) REVERT: A 123 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7276 (mtmt) REVERT: A 130 GLN cc_start: 0.7504 (tt0) cc_final: 0.7228 (tt0) REVERT: A 147 TYR cc_start: 0.7723 (m-10) cc_final: 0.7160 (m-80) REVERT: A 176 LYS cc_start: 0.8267 (mttt) cc_final: 0.7949 (mtpp) REVERT: A 205 SER cc_start: 0.8491 (t) cc_final: 0.8106 (p) REVERT: A 241 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6716 (tm-30) REVERT: A 252 LYS cc_start: 0.8742 (tttt) cc_final: 0.8452 (ttmm) REVERT: A 269 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6573 (mt-10) REVERT: A 281 ASP cc_start: 0.7744 (t0) cc_final: 0.7448 (t0) REVERT: A 307 VAL cc_start: 0.8709 (t) cc_final: 0.8466 (p) REVERT: A 332 VAL cc_start: 0.8502 (t) cc_final: 0.8217 (m) REVERT: A 368 GLN cc_start: 0.7240 (tm-30) cc_final: 0.6868 (tm-30) REVERT: B 34 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 37 LYS cc_start: 0.7644 (mmtt) cc_final: 0.7120 (mmtt) REVERT: B 62 LYS cc_start: 0.7195 (tttt) cc_final: 0.6750 (mtpp) REVERT: B 68 TYR cc_start: 0.8629 (p90) cc_final: 0.8265 (p90) REVERT: B 108 ASP cc_start: 0.7438 (p0) cc_final: 0.7031 (p0) REVERT: B 112 MET cc_start: 0.8347 (ttt) cc_final: 0.8115 (ttm) REVERT: B 138 LEU cc_start: 0.8003 (mm) cc_final: 0.7705 (mp) REVERT: B 164 TYR cc_start: 0.8097 (m-80) cc_final: 0.7470 (m-80) REVERT: B 230 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8188 (ptp-110) REVERT: B 254 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7233 (mmmt) REVERT: B 294 TYR cc_start: 0.7919 (m-10) cc_final: 0.7598 (m-10) REVERT: B 324 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7290 (mtmm) REVERT: B 336 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7888 (ttmm) REVERT: C 10 GLN cc_start: 0.7589 (tt0) cc_final: 0.7351 (tt0) REVERT: C 37 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7126 (mtpt) REVERT: C 52 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7448 (ttmt) REVERT: C 107 TYR cc_start: 0.7932 (p90) cc_final: 0.7296 (p90) REVERT: C 120 GLU cc_start: 0.7491 (pt0) cc_final: 0.7058 (pt0) REVERT: C 132 PHE cc_start: 0.7732 (m-10) cc_final: 0.7522 (m-10) REVERT: C 186 ASN cc_start: 0.8169 (m110) cc_final: 0.7892 (m110) REVERT: C 207 THR cc_start: 0.8011 (t) cc_final: 0.7706 (p) REVERT: C 214 TYR cc_start: 0.8289 (t80) cc_final: 0.7828 (t80) REVERT: C 222 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7384 (mt0) REVERT: C 245 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7473 (mtpt) REVERT: C 246 ASP cc_start: 0.6859 (m-30) cc_final: 0.6596 (m-30) REVERT: C 254 THR cc_start: 0.8463 (p) cc_final: 0.8183 (t) REVERT: C 260 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6601 (mt-10) REVERT: C 261 ILE cc_start: 0.8239 (mm) cc_final: 0.7767 (mm) REVERT: C 334 SER cc_start: 0.8557 (t) cc_final: 0.8081 (p) REVERT: C 338 THR cc_start: 0.7939 (m) cc_final: 0.7519 (t) REVERT: D 48 GLN cc_start: 0.7643 (tt0) cc_final: 0.7366 (tt0) REVERT: D 64 ARG cc_start: 0.7208 (mmm-85) cc_final: 0.6875 (mtt-85) REVERT: D 74 ILE cc_start: 0.8251 (mt) cc_final: 0.7965 (mt) REVERT: D 75 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8175 (mttm) REVERT: D 77 ILE cc_start: 0.8305 (mt) cc_final: 0.8069 (tt) REVERT: D 130 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7540 (mtmm) REVERT: D 176 SER cc_start: 0.7942 (p) cc_final: 0.7723 (t) REVERT: D 180 SER cc_start: 0.8229 (p) cc_final: 0.7782 (m) REVERT: D 215 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7490 (ttmm) REVERT: D 227 ARG cc_start: 0.7438 (ttm110) cc_final: 0.6959 (ttm110) REVERT: D 242 LYS cc_start: 0.8145 (mttm) cc_final: 0.7872 (mttm) REVERT: D 254 LYS cc_start: 0.8572 (mtmp) cc_final: 0.8160 (mtpp) REVERT: D 338 PHE cc_start: 0.8098 (m-10) cc_final: 0.7891 (m-80) REVERT: E 6 THR cc_start: 0.8144 (m) cc_final: 0.7709 (p) REVERT: E 47 VAL cc_start: 0.8325 (m) cc_final: 0.8061 (p) REVERT: E 110 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8154 (mtmm) REVERT: E 188 ASP cc_start: 0.6993 (t70) cc_final: 0.6577 (t70) REVERT: E 202 ASP cc_start: 0.8131 (p0) cc_final: 0.7913 (p0) REVERT: E 203 ILE cc_start: 0.8110 (mm) cc_final: 0.7806 (pt) REVERT: E 222 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7773 (mm110) REVERT: E 245 LYS cc_start: 0.7716 (mttt) cc_final: 0.7484 (mtpp) REVERT: E 246 ASP cc_start: 0.7144 (m-30) cc_final: 0.6730 (m-30) REVERT: E 252 LYS cc_start: 0.8125 (tttt) cc_final: 0.7918 (tttt) REVERT: E 262 TYR cc_start: 0.7506 (m-80) cc_final: 0.6181 (m-80) REVERT: E 269 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7000 (mt-10) REVERT: E 280 PHE cc_start: 0.8427 (m-10) cc_final: 0.7942 (m-10) REVERT: E 338 THR cc_start: 0.8541 (m) cc_final: 0.8263 (t) REVERT: E 340 LYS cc_start: 0.7623 (tttt) cc_final: 0.7341 (ttmt) REVERT: F 8 GLU cc_start: 0.7341 (tp30) cc_final: 0.7089 (tp30) REVERT: F 16 MET cc_start: 0.7934 (mtp) cc_final: 0.7679 (mtp) REVERT: F 53 TYR cc_start: 0.8156 (m-80) cc_final: 0.7815 (m-80) REVERT: F 57 SER cc_start: 0.8508 (p) cc_final: 0.8230 (t) REVERT: F 60 ASN cc_start: 0.7926 (m-40) cc_final: 0.7630 (m-40) REVERT: F 69 ASP cc_start: 0.7414 (t70) cc_final: 0.7120 (t70) REVERT: F 75 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7836 (mmtp) REVERT: F 175 ASP cc_start: 0.8324 (t0) cc_final: 0.7848 (t0) REVERT: F 177 SER cc_start: 0.8733 (m) cc_final: 0.8465 (p) REVERT: F 206 LYS cc_start: 0.7518 (mmtt) cc_final: 0.7315 (tptt) REVERT: F 245 LYS cc_start: 0.8125 (ptmt) cc_final: 0.7799 (ptmm) REVERT: F 261 LEU cc_start: 0.8521 (tp) cc_final: 0.8306 (mt) REVERT: F 286 LYS cc_start: 0.8252 (tppp) cc_final: 0.7948 (tppp) REVERT: F 290 LYS cc_start: 0.7616 (mttt) cc_final: 0.7372 (mttt) REVERT: H 38 ARG cc_start: 0.7149 (ptt-90) cc_final: 0.6722 (ptt-90) REVERT: H 76 ASN cc_start: 0.6260 (p0) cc_final: 0.5479 (p0) REVERT: L 20 THR cc_start: 0.8591 (t) cc_final: 0.8300 (p) REVERT: L 42 LYS cc_start: 0.8249 (mmmt) cc_final: 0.8012 (mmmt) REVERT: L 47 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7797 (mp) REVERT: L 54 LEU cc_start: 0.8699 (tp) cc_final: 0.8444 (tp) outliers start: 63 outliers final: 38 residues processed: 713 average time/residue: 0.3589 time to fit residues: 374.1830 Evaluate side-chains 701 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 661 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 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 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 69 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 GLN 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 57 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 34 GLU 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 237 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 51 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 19 optimal weight: 0.0470 chunk 101 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 241 optimal weight: 2.9990 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 218 ASN A 270 ASN B 168 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN D 160 ASN D 288 HIS D 341 GLN F 41 HIS F 132 ASN F 318 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103344 restraints weight = 30257.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106302 restraints weight = 12956.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108048 restraints weight = 6787.277| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 19687 Z= 0.268 Angle : 0.694 11.598 26822 Z= 0.361 Chirality : 0.047 0.244 2935 Planarity : 0.005 0.049 3462 Dihedral : 5.759 28.964 2674 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 4.47 % Allowed : 14.99 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.16), residues: 2445 helix: -2.32 (0.61), residues: 48 sheet: -0.90 (0.17), residues: 921 loop : -2.08 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 103 HIS 0.012 0.002 HIS C 362 PHE 0.025 0.002 PHE C 356 TYR 0.043 0.002 TYR F 9 ARG 0.005 0.001 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 493) hydrogen bonds : angle 5.34901 ( 1251) SS BOND : bond 0.00426 ( 40) SS BOND : angle 1.47852 ( 80) covalent geometry : bond 0.00611 (19647) covalent geometry : angle 0.68997 (26742) *********************** 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 782 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 688 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7673 (t) cc_final: 0.7355 (t) REVERT: A 30 SER cc_start: 0.8239 (m) cc_final: 0.7741 (p) REVERT: A 35 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7665 (ttmm) REVERT: A 37 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7971 (mtmm) REVERT: A 42 VAL cc_start: 0.8599 (t) cc_final: 0.8116 (m) REVERT: A 45 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6768 (mm-30) REVERT: A 52 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8074 (ttpp) REVERT: A 75 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: A 76 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6315 (tm-30) REVERT: A 105 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7765 (mtpp) REVERT: A 123 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7487 (mtmt) REVERT: A 130 GLN cc_start: 0.7510 (tt0) cc_final: 0.7267 (tt0) REVERT: A 136 THR cc_start: 0.7454 (m) cc_final: 0.7105 (p) REVERT: A 147 TYR cc_start: 0.7823 (m-10) cc_final: 0.7369 (m-10) REVERT: A 176 LYS cc_start: 0.8251 (mttt) cc_final: 0.7955 (mtpp) REVERT: A 205 SER cc_start: 0.8573 (t) cc_final: 0.8109 (p) REVERT: A 241 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6825 (tm-30) REVERT: A 252 LYS cc_start: 0.8745 (tttt) cc_final: 0.8507 (ttmm) REVERT: A 269 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6710 (mt-10) REVERT: A 281 ASP cc_start: 0.7819 (t0) cc_final: 0.7526 (t0) REVERT: A 368 GLN cc_start: 0.7268 (tm-30) cc_final: 0.6959 (tm-30) REVERT: B 34 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6916 (mm-30) REVERT: B 37 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7479 (mmtt) REVERT: B 68 TYR cc_start: 0.8681 (p90) cc_final: 0.8372 (p90) REVERT: B 108 ASP cc_start: 0.7451 (p0) cc_final: 0.7032 (p0) REVERT: B 138 LEU cc_start: 0.8215 (mm) cc_final: 0.7944 (mt) REVERT: B 164 TYR cc_start: 0.8300 (m-80) cc_final: 0.7507 (m-80) REVERT: B 213 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7788 (mmtm) REVERT: B 230 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8012 (ttm110) REVERT: B 265 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7494 (mmtt) REVERT: B 290 LYS cc_start: 0.7306 (ttmt) cc_final: 0.6996 (ttmt) REVERT: B 324 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7424 (mtmm) REVERT: B 336 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7867 (ttmm) REVERT: C 10 GLN cc_start: 0.7586 (tt0) cc_final: 0.7360 (tt0) REVERT: C 132 PHE cc_start: 0.7653 (m-10) cc_final: 0.7410 (m-10) REVERT: C 207 THR cc_start: 0.8015 (t) cc_final: 0.7730 (p) REVERT: C 214 TYR cc_start: 0.8365 (t80) cc_final: 0.7754 (t80) REVERT: C 222 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: C 235 GLN cc_start: 0.7887 (pt0) cc_final: 0.7614 (pt0) REVERT: C 242 GLN cc_start: 0.7804 (tp40) cc_final: 0.7468 (tp40) REVERT: C 245 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7505 (mtpt) REVERT: C 338 THR cc_start: 0.8079 (m) cc_final: 0.7663 (t) REVERT: D 74 ILE cc_start: 0.8247 (mt) cc_final: 0.7922 (mt) REVERT: D 75 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8150 (mttm) REVERT: D 77 ILE cc_start: 0.8348 (mt) cc_final: 0.8073 (tt) REVERT: D 120 ARG cc_start: 0.6870 (tpt-90) cc_final: 0.6569 (tpt-90) REVERT: D 130 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7723 (mtmm) REVERT: D 180 SER cc_start: 0.8212 (p) cc_final: 0.7707 (m) REVERT: D 215 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7478 (ttmm) REVERT: D 254 LYS cc_start: 0.8625 (mtmp) cc_final: 0.8231 (mtpp) REVERT: D 261 LEU cc_start: 0.8728 (tp) cc_final: 0.8081 (mt) REVERT: D 338 PHE cc_start: 0.8067 (m-10) cc_final: 0.7853 (m-80) REVERT: E 6 THR cc_start: 0.8209 (m) cc_final: 0.7757 (p) REVERT: E 77 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7059 (mt0) REVERT: E 110 LYS cc_start: 0.8494 (ptpp) cc_final: 0.8229 (mtmm) REVERT: E 161 ILE cc_start: 0.7770 (mt) cc_final: 0.7558 (mt) REVERT: E 188 ASP cc_start: 0.6997 (t70) cc_final: 0.6598 (t70) REVERT: E 202 ASP cc_start: 0.8213 (p0) cc_final: 0.7912 (p0) REVERT: E 203 ILE cc_start: 0.8133 (mm) cc_final: 0.7623 (tt) REVERT: E 222 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7645 (mt0) REVERT: E 280 PHE cc_start: 0.8443 (m-10) cc_final: 0.8039 (m-10) REVERT: E 324 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7879 (mtmm) REVERT: E 338 THR cc_start: 0.8630 (m) cc_final: 0.8375 (t) REVERT: E 340 LYS cc_start: 0.7742 (tttt) cc_final: 0.7388 (ttmt) REVERT: E 349 GLN cc_start: 0.7200 (tp40) cc_final: 0.6626 (tp40) REVERT: E 386 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.7043 (p-80) REVERT: F 8 GLU cc_start: 0.7324 (tp30) cc_final: 0.6992 (tp30) REVERT: F 16 MET cc_start: 0.7962 (mtp) cc_final: 0.7749 (mtp) REVERT: F 37 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7313 (mmtm) REVERT: F 57 SER cc_start: 0.8477 (p) cc_final: 0.8035 (t) REVERT: F 60 ASN cc_start: 0.8083 (m-40) cc_final: 0.7732 (m-40) REVERT: F 69 ASP cc_start: 0.7475 (t70) cc_final: 0.7181 (t70) REVERT: F 75 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7679 (mmtp) REVERT: F 76 GLU cc_start: 0.6613 (tp30) cc_final: 0.6360 (tp30) REVERT: F 115 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7434 (mttm) REVERT: F 129 VAL cc_start: 0.8252 (t) cc_final: 0.7938 (p) REVERT: F 175 ASP cc_start: 0.8362 (t0) cc_final: 0.8005 (t0) REVERT: F 177 SER cc_start: 0.8778 (m) cc_final: 0.8451 (p) REVERT: F 197 LEU cc_start: 0.8008 (tp) cc_final: 0.7792 (tp) REVERT: F 227 ARG cc_start: 0.7441 (tpp80) cc_final: 0.7205 (mmt-90) REVERT: F 254 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7851 (mtmt) REVERT: F 261 LEU cc_start: 0.8554 (tp) cc_final: 0.8323 (mt) REVERT: F 286 LYS cc_start: 0.8296 (tppp) cc_final: 0.8081 (tppp) REVERT: F 290 LYS cc_start: 0.7742 (mttt) cc_final: 0.7490 (mttt) REVERT: H 38 ARG cc_start: 0.7198 (ptt-90) cc_final: 0.6865 (ptt-90) REVERT: H 76 ASN cc_start: 0.6672 (p0) cc_final: 0.5938 (p0) REVERT: H 83 LYS cc_start: 0.8389 (tmtt) cc_final: 0.8121 (tmtt) REVERT: L 20 THR cc_start: 0.8582 (t) cc_final: 0.8250 (p) REVERT: L 42 LYS cc_start: 0.8274 (mmmt) cc_final: 0.8027 (mmmt) REVERT: L 47 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8029 (mt) REVERT: L 90 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6382 (tm130) outliers start: 94 outliers final: 66 residues processed: 732 average time/residue: 0.3464 time to fit residues: 371.8773 Evaluate side-chains 736 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 665 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 296 LEU 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 73 THR Chi-restraints excluded: chain B residue 76 GLU 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 55 MET 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 135 ILE Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 251 LEU 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 49 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 82 VAL 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 270 LEU Chi-restraints excluded: chain D residue 297 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 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 168 THR Chi-restraints excluded: chain E residue 207 THR 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 34 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 119 VAL 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 273 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 87 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 196 GLN A 218 ASN A 235 GLN A 270 ASN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 160 ASN E 102 GLN F 305 HIS F 318 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102610 restraints weight = 30290.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105574 restraints weight = 12974.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107327 restraints weight = 6789.335| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 19687 Z= 0.272 Angle : 0.699 10.627 26822 Z= 0.365 Chirality : 0.047 0.182 2935 Planarity : 0.005 0.044 3462 Dihedral : 5.829 28.845 2674 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.06 % Favored : 91.86 % Rotamer: Outliers : 4.43 % Allowed : 16.47 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.16), residues: 2445 helix: -2.39 (0.60), residues: 48 sheet: -0.88 (0.17), residues: 919 loop : -2.03 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.025 0.002 HIS B 168 PHE 0.024 0.002 PHE C 356 TYR 0.042 0.002 TYR F 9 ARG 0.006 0.001 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 493) hydrogen bonds : angle 5.37016 ( 1251) SS BOND : bond 0.00446 ( 40) SS BOND : angle 1.51743 ( 80) covalent geometry : bond 0.00620 (19647) covalent geometry : angle 0.69546 (26742) *********************** 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 764 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 671 time to evaluate : 1.971 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: 0.7633 (t) cc_final: 0.7310 (t) REVERT: A 18 ILE cc_start: 0.8240 (pt) cc_final: 0.8013 (mm) REVERT: A 30 SER cc_start: 0.8192 (m) cc_final: 0.7712 (p) REVERT: A 35 LYS cc_start: 0.8397 (ttmt) cc_final: 0.7699 (ttmm) REVERT: A 37 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7957 (mtmm) REVERT: A 42 VAL cc_start: 0.8607 (t) cc_final: 0.8131 (m) REVERT: A 45 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6763 (mm-30) REVERT: A 52 LYS cc_start: 0.8327 (ttpt) cc_final: 0.8028 (ttpp) REVERT: A 75 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: A 76 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6358 (tm-30) REVERT: A 105 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7756 (mtpp) REVERT: A 123 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7488 (mtmt) REVERT: A 130 GLN cc_start: 0.7511 (tt0) cc_final: 0.7276 (tt0) REVERT: A 136 THR cc_start: 0.7411 (m) cc_final: 0.7050 (p) REVERT: A 147 TYR cc_start: 0.7835 (m-10) cc_final: 0.7462 (m-10) REVERT: A 176 LYS cc_start: 0.8247 (mttt) cc_final: 0.7956 (mtpp) REVERT: A 205 SER cc_start: 0.8587 (t) cc_final: 0.8140 (p) REVERT: A 241 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6832 (tm-30) REVERT: A 269 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6708 (mt-10) REVERT: A 281 ASP cc_start: 0.7809 (t0) cc_final: 0.7471 (t0) REVERT: A 368 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 18 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7595 (ptm-80) REVERT: B 34 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7087 (mm-30) REVERT: B 37 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7505 (mmtt) REVERT: B 68 TYR cc_start: 0.8675 (p90) cc_final: 0.8313 (p90) REVERT: B 108 ASP cc_start: 0.7453 (p0) cc_final: 0.7074 (p0) REVERT: B 138 LEU cc_start: 0.8204 (mm) cc_final: 0.7918 (mt) REVERT: B 164 TYR cc_start: 0.8372 (m-80) cc_final: 0.7588 (m-80) REVERT: B 213 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7486 (mmtm) REVERT: B 230 ARG cc_start: 0.8462 (mtp85) cc_final: 0.7894 (ttm110) REVERT: B 265 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7453 (mmtt) REVERT: B 283 VAL cc_start: 0.8257 (t) cc_final: 0.7979 (m) REVERT: B 290 LYS cc_start: 0.7315 (ttmt) cc_final: 0.7026 (ttmt) REVERT: B 302 ASP cc_start: 0.6802 (p0) cc_final: 0.6553 (p0) REVERT: B 324 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7426 (mtmm) REVERT: B 336 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7812 (ttmm) REVERT: C 10 GLN cc_start: 0.7586 (tt0) cc_final: 0.7335 (tt0) REVERT: C 120 GLU cc_start: 0.7709 (pt0) cc_final: 0.7469 (pt0) REVERT: C 132 PHE cc_start: 0.7621 (m-10) cc_final: 0.7319 (m-10) REVERT: C 184 ILE cc_start: 0.8559 (mm) cc_final: 0.8154 (mt) REVERT: C 186 ASN cc_start: 0.8201 (m-40) cc_final: 0.7909 (m-40) REVERT: C 207 THR cc_start: 0.7984 (t) cc_final: 0.7701 (p) REVERT: C 214 TYR cc_start: 0.8412 (t80) cc_final: 0.7804 (t80) REVERT: C 222 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7550 (mt0) REVERT: C 245 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7569 (mtpt) REVERT: C 288 THR cc_start: 0.6758 (OUTLIER) cc_final: 0.6408 (p) REVERT: C 338 THR cc_start: 0.8078 (m) cc_final: 0.7688 (t) REVERT: C 394 HIS cc_start: 0.7375 (p90) cc_final: 0.7155 (p90) REVERT: D 74 ILE cc_start: 0.8249 (mt) cc_final: 0.7879 (mt) REVERT: D 75 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8078 (mttm) REVERT: D 77 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8083 (tt) REVERT: D 120 ARG cc_start: 0.6876 (tpt-90) cc_final: 0.6542 (tpt-90) REVERT: D 130 LYS cc_start: 0.8004 (mtmm) cc_final: 0.7587 (mtmm) REVERT: D 180 SER cc_start: 0.8163 (p) cc_final: 0.7569 (m) REVERT: D 215 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7524 (ttmm) REVERT: D 227 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7190 (tpp80) REVERT: D 241 ASP cc_start: 0.7582 (p0) cc_final: 0.7368 (p0) REVERT: D 257 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8630 (m) REVERT: D 354 GLU cc_start: 0.5414 (OUTLIER) cc_final: 0.2915 (tp30) REVERT: E 6 THR cc_start: 0.8215 (m) cc_final: 0.7765 (p) REVERT: E 110 LYS cc_start: 0.8488 (ptpp) cc_final: 0.8251 (mtmm) REVERT: E 161 ILE cc_start: 0.7774 (mt) cc_final: 0.7544 (mt) REVERT: E 188 ASP cc_start: 0.7021 (t70) cc_final: 0.6616 (t70) REVERT: E 202 ASP cc_start: 0.8238 (p0) cc_final: 0.7899 (p0) REVERT: E 203 ILE cc_start: 0.8141 (mm) cc_final: 0.7641 (tt) REVERT: E 222 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7664 (mt0) REVERT: E 280 PHE cc_start: 0.8428 (m-10) cc_final: 0.8010 (m-10) REVERT: E 300 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: E 324 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7832 (mtmm) REVERT: E 338 THR cc_start: 0.8649 (m) cc_final: 0.8363 (t) REVERT: E 340 LYS cc_start: 0.7751 (tttt) cc_final: 0.7418 (ttmt) REVERT: E 349 GLN cc_start: 0.7234 (tp40) cc_final: 0.6645 (tp40) REVERT: E 386 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7109 (p-80) REVERT: F 16 MET cc_start: 0.7955 (mtp) cc_final: 0.7732 (mtp) REVERT: F 60 ASN cc_start: 0.8111 (m-40) cc_final: 0.7779 (m-40) REVERT: F 69 ASP cc_start: 0.7430 (t70) cc_final: 0.7128 (t70) REVERT: F 75 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8093 (mmtp) REVERT: F 115 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7544 (mttm) REVERT: F 129 VAL cc_start: 0.8233 (t) cc_final: 0.7904 (p) REVERT: F 177 SER cc_start: 0.8781 (m) cc_final: 0.8408 (p) REVERT: F 261 LEU cc_start: 0.8570 (tp) cc_final: 0.8342 (mt) REVERT: F 286 LYS cc_start: 0.8282 (tppp) cc_final: 0.8081 (tppp) REVERT: F 290 LYS cc_start: 0.7750 (mttt) cc_final: 0.7512 (mttt) REVERT: H 38 ARG cc_start: 0.7266 (ptt-90) cc_final: 0.6921 (ptt-90) REVERT: H 52 LYS cc_start: 0.8256 (tptp) cc_final: 0.7923 (tptp) REVERT: H 76 ASN cc_start: 0.6734 (p0) cc_final: 0.6003 (p0) REVERT: H 83 LYS cc_start: 0.8385 (tmtt) cc_final: 0.8110 (tptp) REVERT: L 20 THR cc_start: 0.8604 (t) cc_final: 0.8261 (p) REVERT: L 42 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8049 (mmmt) REVERT: L 90 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6416 (tm130) outliers start: 93 outliers final: 62 residues processed: 717 average time/residue: 0.3399 time to fit residues: 356.1178 Evaluate side-chains 738 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 667 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 152 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 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 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 69 THR Chi-restraints excluded: chain C residue 79 LYS 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 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 110 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 179 VAL 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 297 THR Chi-restraints excluded: chain D residue 311 ILE 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 69 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 168 THR 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 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 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 273 GLU 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 Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 104 optimal weight: 7.9990 chunk 131 optimal weight: 0.4980 chunk 142 optimal weight: 0.5980 chunk 200 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 152 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 218 ASN A 270 ASN C 270 ASN E 204 GLN E 349 GLN F 318 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103808 restraints weight = 30581.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106786 restraints weight = 13191.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108529 restraints weight = 6913.894| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19687 Z= 0.134 Angle : 0.613 9.285 26822 Z= 0.319 Chirality : 0.044 0.170 2935 Planarity : 0.004 0.042 3462 Dihedral : 5.340 26.177 2674 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.99 % Favored : 92.97 % Rotamer: Outliers : 3.38 % Allowed : 18.28 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2445 helix: -2.34 (0.63), residues: 48 sheet: -0.73 (0.17), residues: 910 loop : -1.84 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 330 HIS 0.006 0.001 HIS F 168 PHE 0.027 0.002 PHE C 356 TYR 0.037 0.001 TYR F 9 ARG 0.003 0.000 ARG F 298 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 493) hydrogen bonds : angle 5.16633 ( 1251) SS BOND : bond 0.00270 ( 40) SS BOND : angle 1.17206 ( 80) covalent geometry : bond 0.00309 (19647) covalent geometry : angle 0.61069 (26742) *********************** 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 746 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 675 time to evaluate : 2.051 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 9 SER cc_start: 0.7641 (t) cc_final: 0.7332 (t) REVERT: A 30 SER cc_start: 0.8121 (m) cc_final: 0.7697 (p) REVERT: A 35 LYS cc_start: 0.8403 (ttmt) cc_final: 0.7960 (ttmm) REVERT: A 37 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7920 (mtmm) REVERT: A 42 VAL cc_start: 0.8469 (t) cc_final: 0.8029 (m) REVERT: A 45 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6742 (mm-30) REVERT: A 52 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7983 (ttpp) REVERT: A 76 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6318 (tm-30) REVERT: A 105 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7716 (mtpp) REVERT: A 111 SER cc_start: 0.8414 (p) cc_final: 0.7974 (t) REVERT: A 123 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7387 (mtmt) REVERT: A 147 TYR cc_start: 0.7757 (m-10) cc_final: 0.7446 (m-10) REVERT: A 176 LYS cc_start: 0.8272 (mttt) cc_final: 0.7913 (mtpp) REVERT: A 205 SER cc_start: 0.8522 (t) cc_final: 0.8114 (p) REVERT: A 241 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 281 ASP cc_start: 0.7768 (t0) cc_final: 0.7372 (t0) REVERT: B 18 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7641 (ptm-80) REVERT: B 34 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 37 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7102 (mmtt) REVERT: B 62 LYS cc_start: 0.7454 (tttt) cc_final: 0.6964 (mtpp) REVERT: B 68 TYR cc_start: 0.8682 (p90) cc_final: 0.8353 (p90) REVERT: B 108 ASP cc_start: 0.7490 (p0) cc_final: 0.7074 (p0) REVERT: B 164 TYR cc_start: 0.8302 (m-80) cc_final: 0.7458 (m-80) REVERT: B 175 ASP cc_start: 0.6779 (t0) cc_final: 0.6485 (m-30) REVERT: B 213 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7483 (mmtm) REVERT: B 230 ARG cc_start: 0.8414 (mtp85) cc_final: 0.8137 (ptp-110) REVERT: B 265 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7568 (mmtt) REVERT: B 283 VAL cc_start: 0.8306 (t) cc_final: 0.8026 (m) REVERT: B 324 LYS cc_start: 0.7636 (mtmm) cc_final: 0.7352 (mtmm) REVERT: B 336 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7783 (ttmm) REVERT: C 10 GLN cc_start: 0.7594 (tt0) cc_final: 0.7341 (tt0) REVERT: C 35 LYS cc_start: 0.8253 (tttt) cc_final: 0.7967 (tptm) REVERT: C 120 GLU cc_start: 0.7652 (pt0) cc_final: 0.7110 (pt0) REVERT: C 132 PHE cc_start: 0.7625 (m-10) cc_final: 0.7319 (m-10) REVERT: C 184 ILE cc_start: 0.8475 (mm) cc_final: 0.7916 (mt) REVERT: C 207 THR cc_start: 0.7982 (t) cc_final: 0.7712 (p) REVERT: C 214 TYR cc_start: 0.8388 (t80) cc_final: 0.7687 (t80) REVERT: C 222 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: C 245 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7575 (mtpt) REVERT: C 266 ILE cc_start: 0.8398 (mt) cc_final: 0.8090 (mm) REVERT: C 288 THR cc_start: 0.6535 (OUTLIER) cc_final: 0.6173 (p) REVERT: C 338 THR cc_start: 0.8060 (m) cc_final: 0.7678 (t) REVERT: D 64 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6916 (mtp85) REVERT: D 74 ILE cc_start: 0.8184 (mt) cc_final: 0.7836 (mt) REVERT: D 75 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8015 (mttm) REVERT: D 77 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8121 (tt) REVERT: D 130 LYS cc_start: 0.7972 (mtmm) cc_final: 0.7702 (mtmm) REVERT: D 180 SER cc_start: 0.8264 (p) cc_final: 0.7642 (m) REVERT: D 215 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7466 (ttmm) REVERT: D 227 ARG cc_start: 0.7681 (ttm110) cc_final: 0.6991 (tpp80) REVERT: D 257 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8629 (m) REVERT: D 354 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.2960 (tp30) REVERT: E 6 THR cc_start: 0.8137 (m) cc_final: 0.7739 (p) REVERT: E 77 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7031 (mt0) REVERT: E 87 PHE cc_start: 0.7929 (m-80) cc_final: 0.7681 (m-80) REVERT: E 161 ILE cc_start: 0.7653 (mt) cc_final: 0.7409 (mt) REVERT: E 188 ASP cc_start: 0.7019 (t70) cc_final: 0.6652 (t70) REVERT: E 202 ASP cc_start: 0.8210 (p0) cc_final: 0.7978 (p0) REVERT: E 203 ILE cc_start: 0.8070 (mm) cc_final: 0.7800 (pt) REVERT: E 222 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7696 (mt0) REVERT: E 262 TYR cc_start: 0.7385 (m-80) cc_final: 0.6545 (m-80) REVERT: E 280 PHE cc_start: 0.8388 (m-10) cc_final: 0.7887 (m-10) REVERT: E 300 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: E 324 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7854 (mtmm) REVERT: E 338 THR cc_start: 0.8650 (m) cc_final: 0.8308 (t) REVERT: E 340 LYS cc_start: 0.7706 (tttt) cc_final: 0.7388 (ttmt) REVERT: F 8 GLU cc_start: 0.7332 (tp30) cc_final: 0.7007 (tp30) REVERT: F 16 MET cc_start: 0.7961 (mtp) cc_final: 0.7739 (mtp) REVERT: F 37 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7312 (mmtm) REVERT: F 57 SER cc_start: 0.8532 (p) cc_final: 0.8267 (t) REVERT: F 69 ASP cc_start: 0.7332 (t70) cc_final: 0.7027 (t70) REVERT: F 75 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7633 (mmtp) REVERT: F 76 GLU cc_start: 0.6604 (tp30) cc_final: 0.6259 (tp30) REVERT: F 115 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7485 (mttm) REVERT: F 129 VAL cc_start: 0.8181 (t) cc_final: 0.7804 (p) REVERT: F 177 SER cc_start: 0.8815 (m) cc_final: 0.8430 (p) REVERT: F 261 LEU cc_start: 0.8514 (tp) cc_final: 0.8309 (mt) REVERT: F 290 LYS cc_start: 0.7679 (mttt) cc_final: 0.7448 (mttt) REVERT: H 38 ARG cc_start: 0.7253 (ptt-90) cc_final: 0.6884 (ptt-90) REVERT: H 76 ASN cc_start: 0.6449 (p0) cc_final: 0.5694 (p0) REVERT: H 83 LYS cc_start: 0.8343 (tmtt) cc_final: 0.8025 (tptp) REVERT: L 20 THR cc_start: 0.8643 (t) cc_final: 0.8324 (p) REVERT: L 42 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7990 (mmmt) outliers start: 71 outliers final: 53 residues processed: 707 average time/residue: 0.3675 time to fit residues: 384.1208 Evaluate side-chains 717 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 658 time to evaluate : 2.409 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU 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 61 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 79 LYS 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 288 THR 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 77 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 207 ILE 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 297 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 65 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 168 THR 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 11 LEU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 GLN 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 273 GLU 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 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 223 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 234 optimal weight: 0.3980 chunk 207 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 218 ASN A 270 ASN A 368 GLN B 168 HIS B 308 HIS C 157 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 270 ASN E 204 GLN F 288 HIS F 318 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104927 restraints weight = 30135.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107881 restraints weight = 12887.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109599 restraints weight = 6761.271| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19687 Z= 0.145 Angle : 0.625 8.974 26822 Z= 0.324 Chirality : 0.045 0.199 2935 Planarity : 0.004 0.049 3462 Dihedral : 5.265 27.209 2674 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.12 % Favored : 92.84 % Rotamer: Outliers : 4.43 % Allowed : 18.04 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2445 helix: -2.26 (0.63), residues: 48 sheet: -0.58 (0.17), residues: 892 loop : -1.77 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 330 HIS 0.007 0.001 HIS C 394 PHE 0.026 0.002 PHE C 356 TYR 0.031 0.001 TYR F 9 ARG 0.003 0.000 ARG F 298 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 493) hydrogen bonds : angle 5.14599 ( 1251) SS BOND : bond 0.00282 ( 40) SS BOND : angle 1.32155 ( 80) covalent geometry : bond 0.00337 (19647) covalent geometry : angle 0.62146 (26742) *********************** 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 755 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 662 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7645 (t) cc_final: 0.7265 (t) REVERT: A 30 SER cc_start: 0.8130 (m) cc_final: 0.7676 (p) REVERT: A 35 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7989 (ttmm) REVERT: A 37 LYS cc_start: 0.8333 (mtmm) cc_final: 0.7899 (mtmm) REVERT: A 45 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6791 (mm-30) REVERT: A 52 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7955 (ttpp) REVERT: A 76 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6383 (tm-30) REVERT: A 105 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7729 (mtpp) REVERT: A 111 SER cc_start: 0.8427 (p) cc_final: 0.8082 (t) REVERT: A 123 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7426 (mtmt) REVERT: A 136 THR cc_start: 0.7473 (m) cc_final: 0.7061 (p) REVERT: A 147 TYR cc_start: 0.7767 (m-10) cc_final: 0.7374 (m-80) REVERT: A 176 LYS cc_start: 0.8260 (mttt) cc_final: 0.7923 (mtpp) REVERT: A 205 SER cc_start: 0.8551 (t) cc_final: 0.8138 (p) REVERT: A 241 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6752 (tm-30) REVERT: A 273 VAL cc_start: 0.8699 (p) cc_final: 0.8471 (p) REVERT: A 281 ASP cc_start: 0.7742 (t0) cc_final: 0.7369 (t0) REVERT: B 18 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7632 (ptm-80) REVERT: B 34 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7069 (mm-30) REVERT: B 62 LYS cc_start: 0.7462 (tttt) cc_final: 0.6960 (mtpp) REVERT: B 68 TYR cc_start: 0.8698 (p90) cc_final: 0.8428 (p90) REVERT: B 108 ASP cc_start: 0.7451 (p0) cc_final: 0.7046 (p0) REVERT: B 164 TYR cc_start: 0.8305 (m-80) cc_final: 0.7491 (m-80) REVERT: B 175 ASP cc_start: 0.6714 (t0) cc_final: 0.6359 (m-30) REVERT: B 230 ARG cc_start: 0.8419 (mtp85) cc_final: 0.8048 (ptp-110) REVERT: B 265 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7558 (mmtt) REVERT: B 283 VAL cc_start: 0.8309 (t) cc_final: 0.8041 (m) REVERT: B 294 TYR cc_start: 0.8268 (m-10) cc_final: 0.7483 (m-80) REVERT: B 324 LYS cc_start: 0.7592 (mtmm) cc_final: 0.7328 (mtmm) REVERT: B 336 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7785 (ttmm) REVERT: C 10 GLN cc_start: 0.7569 (tt0) cc_final: 0.7326 (tt0) REVERT: C 35 LYS cc_start: 0.8227 (tttt) cc_final: 0.7975 (tptp) REVERT: C 120 GLU cc_start: 0.7639 (pt0) cc_final: 0.7191 (pt0) REVERT: C 132 PHE cc_start: 0.7619 (m-10) cc_final: 0.7289 (m-10) REVERT: C 174 ASP cc_start: 0.7654 (t70) cc_final: 0.7396 (t0) REVERT: C 184 ILE cc_start: 0.8493 (mm) cc_final: 0.7975 (mt) REVERT: C 207 THR cc_start: 0.7998 (t) cc_final: 0.7725 (p) REVERT: C 214 TYR cc_start: 0.8430 (t80) cc_final: 0.7697 (t80) REVERT: C 222 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: C 266 ILE cc_start: 0.8398 (mt) cc_final: 0.8104 (mm) REVERT: C 269 GLU cc_start: 0.7217 (pt0) cc_final: 0.6592 (pt0) REVERT: C 288 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.6122 (p) REVERT: C 338 THR cc_start: 0.8103 (m) cc_final: 0.7719 (t) REVERT: D 74 ILE cc_start: 0.8168 (mt) cc_final: 0.7909 (mt) REVERT: D 77 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8110 (tt) REVERT: D 120 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6476 (ttt-90) REVERT: D 130 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7635 (mtmm) REVERT: D 180 SER cc_start: 0.8272 (p) cc_final: 0.7665 (m) REVERT: D 215 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7464 (ttmm) REVERT: D 227 ARG cc_start: 0.7699 (ttm110) cc_final: 0.7002 (tpp80) REVERT: D 242 LYS cc_start: 0.8144 (mttm) cc_final: 0.7880 (mttm) REVERT: D 257 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8624 (m) REVERT: D 354 GLU cc_start: 0.5347 (OUTLIER) cc_final: 0.2881 (tp30) REVERT: E 6 THR cc_start: 0.8124 (m) cc_final: 0.7767 (p) REVERT: E 77 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7055 (mt0) REVERT: E 87 PHE cc_start: 0.7913 (m-80) cc_final: 0.7622 (m-80) REVERT: E 161 ILE cc_start: 0.7672 (mt) cc_final: 0.7448 (mt) REVERT: E 188 ASP cc_start: 0.7015 (t70) cc_final: 0.6656 (t70) REVERT: E 202 ASP cc_start: 0.8171 (p0) cc_final: 0.7949 (p0) REVERT: E 203 ILE cc_start: 0.8072 (mm) cc_final: 0.7827 (pt) REVERT: E 222 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7663 (mt0) REVERT: E 260 GLU cc_start: 0.6405 (mt-10) cc_final: 0.6115 (mt-10) REVERT: E 262 TYR cc_start: 0.7461 (m-80) cc_final: 0.6531 (m-80) REVERT: E 280 PHE cc_start: 0.8416 (m-10) cc_final: 0.7925 (m-10) REVERT: E 300 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: E 324 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7901 (mtmm) REVERT: E 338 THR cc_start: 0.8630 (m) cc_final: 0.8310 (t) REVERT: E 340 LYS cc_start: 0.7690 (tttt) cc_final: 0.7373 (ttmt) REVERT: F 16 MET cc_start: 0.7989 (mtp) cc_final: 0.7774 (mtp) REVERT: F 37 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7326 (mmtm) REVERT: F 57 SER cc_start: 0.8528 (p) cc_final: 0.8282 (t) REVERT: F 60 ASN cc_start: 0.7932 (m-40) cc_final: 0.7625 (m-40) REVERT: F 69 ASP cc_start: 0.7280 (t70) cc_final: 0.6979 (t70) REVERT: F 75 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7672 (mmtp) REVERT: F 76 GLU cc_start: 0.6608 (tp30) cc_final: 0.6281 (tp30) REVERT: F 115 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7399 (mttm) REVERT: F 129 VAL cc_start: 0.8215 (t) cc_final: 0.7852 (p) REVERT: F 177 SER cc_start: 0.8856 (m) cc_final: 0.8464 (p) REVERT: F 261 LEU cc_start: 0.8514 (tp) cc_final: 0.8307 (mt) REVERT: F 290 LYS cc_start: 0.7678 (mttt) cc_final: 0.7451 (mttt) REVERT: H 38 ARG cc_start: 0.7245 (ptt-90) cc_final: 0.6876 (ptt-90) REVERT: H 76 ASN cc_start: 0.6535 (p0) cc_final: 0.5793 (p0) REVERT: H 83 LYS cc_start: 0.8321 (tmtt) cc_final: 0.8024 (tptp) REVERT: L 20 THR cc_start: 0.8614 (t) cc_final: 0.8301 (p) REVERT: L 42 LYS cc_start: 0.8284 (mmmt) cc_final: 0.8040 (mmmt) REVERT: L 90 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6403 (tm130) outliers start: 93 outliers final: 62 residues processed: 702 average time/residue: 0.3525 time to fit residues: 360.0872 Evaluate side-chains 726 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 656 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 307 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 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 66 GLN Chi-restraints excluded: chain C residue 79 LYS 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 220 VAL 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 20 ILE 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 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 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 168 THR 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 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 48 GLN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 277 THR 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 Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 97 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 155 optimal weight: 0.0050 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 198 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 218 ASN A 270 ASN B 168 HIS C 157 ASN C 218 ASN C 235 GLN C 270 ASN E 368 GLN F 318 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104457 restraints weight = 30761.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107426 restraints weight = 13279.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109153 restraints weight = 6961.670| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19687 Z= 0.120 Angle : 0.620 8.883 26822 Z= 0.318 Chirality : 0.044 0.169 2935 Planarity : 0.004 0.044 3462 Dihedral : 5.108 26.180 2674 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.95 % Favored : 93.01 % Rotamer: Outliers : 3.86 % Allowed : 19.09 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2445 helix: -2.19 (0.63), residues: 49 sheet: -0.50 (0.17), residues: 888 loop : -1.69 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.011 0.001 HIS C 394 PHE 0.026 0.001 PHE C 356 TYR 0.034 0.001 TYR F 9 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 493) hydrogen bonds : angle 5.09532 ( 1251) SS BOND : bond 0.00249 ( 40) SS BOND : angle 1.32227 ( 80) covalent geometry : bond 0.00281 (19647) covalent geometry : angle 0.61646 (26742) *********************** 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 738 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 657 time to evaluate : 3.314 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 9 SER cc_start: 0.7590 (t) cc_final: 0.7256 (t) REVERT: A 30 SER cc_start: 0.8091 (m) cc_final: 0.7695 (p) REVERT: A 35 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8069 (ttmm) REVERT: A 45 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6781 (mm-30) REVERT: A 52 LYS cc_start: 0.8308 (ttpt) cc_final: 0.7940 (ttpp) REVERT: A 76 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6344 (tm-30) REVERT: A 105 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7709 (mtpp) REVERT: A 108 VAL cc_start: 0.8925 (t) cc_final: 0.8424 (m) REVERT: A 110 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8425 (mtmm) REVERT: A 111 SER cc_start: 0.8423 (p) cc_final: 0.8091 (t) REVERT: A 123 LYS cc_start: 0.7663 (mtmt) cc_final: 0.7352 (mtmt) REVERT: A 147 TYR cc_start: 0.7763 (m-10) cc_final: 0.7394 (m-80) REVERT: A 176 LYS cc_start: 0.8280 (mttt) cc_final: 0.7922 (mtpp) REVERT: A 205 SER cc_start: 0.8527 (t) cc_final: 0.8099 (p) REVERT: A 241 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6612 (tm-30) REVERT: A 245 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7299 (mtpp) REVERT: A 273 VAL cc_start: 0.8691 (p) cc_final: 0.8484 (p) REVERT: A 341 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7149 (mm-30) REVERT: B 18 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7596 (ttt-90) REVERT: B 34 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6971 (mm-30) REVERT: B 44 TYR cc_start: 0.8097 (m-80) cc_final: 0.7434 (m-80) REVERT: B 48 GLN cc_start: 0.7570 (tt0) cc_final: 0.7071 (tm-30) REVERT: B 62 LYS cc_start: 0.7463 (tttt) cc_final: 0.6963 (mtpp) REVERT: B 68 TYR cc_start: 0.8684 (p90) cc_final: 0.8462 (p90) REVERT: B 108 ASP cc_start: 0.7483 (p0) cc_final: 0.7051 (p0) REVERT: B 164 TYR cc_start: 0.8292 (m-80) cc_final: 0.7487 (m-80) REVERT: B 175 ASP cc_start: 0.6690 (t0) cc_final: 0.6350 (m-30) REVERT: B 213 LYS cc_start: 0.8135 (mptt) cc_final: 0.7731 (mmmt) REVERT: B 230 ARG cc_start: 0.8395 (mtp85) cc_final: 0.8058 (ptp-110) REVERT: B 265 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7559 (mmtt) REVERT: B 283 VAL cc_start: 0.8282 (t) cc_final: 0.7990 (m) REVERT: B 294 TYR cc_start: 0.8282 (m-10) cc_final: 0.7510 (m-80) REVERT: B 324 LYS cc_start: 0.7595 (mtmm) cc_final: 0.7333 (mtmm) REVERT: B 336 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7836 (ttmm) REVERT: C 10 GLN cc_start: 0.7587 (tt0) cc_final: 0.7310 (tt0) REVERT: C 120 GLU cc_start: 0.7606 (pt0) cc_final: 0.7021 (pt0) REVERT: C 132 PHE cc_start: 0.7625 (m-10) cc_final: 0.7328 (m-10) REVERT: C 178 VAL cc_start: 0.8053 (t) cc_final: 0.7589 (p) REVERT: C 184 ILE cc_start: 0.8537 (mm) cc_final: 0.8027 (mt) REVERT: C 207 THR cc_start: 0.7963 (t) cc_final: 0.7688 (p) REVERT: C 214 TYR cc_start: 0.8433 (t80) cc_final: 0.7624 (t80) REVERT: C 222 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: C 266 ILE cc_start: 0.8398 (mt) cc_final: 0.8097 (mm) REVERT: C 288 THR cc_start: 0.6351 (OUTLIER) cc_final: 0.5993 (p) REVERT: C 338 THR cc_start: 0.8070 (m) cc_final: 0.7683 (t) REVERT: D 64 ARG cc_start: 0.7270 (mmm-85) cc_final: 0.6859 (mtp85) REVERT: D 74 ILE cc_start: 0.8174 (mt) cc_final: 0.7866 (mt) REVERT: D 130 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7639 (mtmm) REVERT: D 147 VAL cc_start: 0.8579 (p) cc_final: 0.8358 (m) REVERT: D 176 SER cc_start: 0.7961 (p) cc_final: 0.7737 (t) REVERT: D 180 SER cc_start: 0.8272 (p) cc_final: 0.7681 (m) REVERT: D 215 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7466 (ttmm) REVERT: D 227 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7246 (tpp80) REVERT: D 242 LYS cc_start: 0.8000 (mttm) cc_final: 0.7609 (mmtp) REVERT: D 257 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8632 (m) REVERT: D 336 LYS cc_start: 0.7838 (mttt) cc_final: 0.7610 (tttt) REVERT: D 354 GLU cc_start: 0.5261 (OUTLIER) cc_final: 0.2747 (tp30) REVERT: E 6 THR cc_start: 0.8144 (m) cc_final: 0.7797 (p) REVERT: E 77 GLN cc_start: 0.7429 (mm-40) cc_final: 0.7044 (mt0) REVERT: E 87 PHE cc_start: 0.7884 (m-80) cc_final: 0.7554 (m-80) REVERT: E 161 ILE cc_start: 0.7640 (mt) cc_final: 0.7407 (mt) REVERT: E 176 LYS cc_start: 0.8051 (mttp) cc_final: 0.7845 (mttp) REVERT: E 188 ASP cc_start: 0.6897 (t70) cc_final: 0.6489 (t70) REVERT: E 202 ASP cc_start: 0.8179 (p0) cc_final: 0.7963 (p0) REVERT: E 203 ILE cc_start: 0.8077 (mm) cc_final: 0.7806 (pt) REVERT: E 222 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7670 (mt0) REVERT: E 246 ASP cc_start: 0.7092 (m-30) cc_final: 0.6787 (m-30) REVERT: E 262 TYR cc_start: 0.7411 (m-80) cc_final: 0.7173 (m-80) REVERT: E 280 PHE cc_start: 0.8434 (m-10) cc_final: 0.7954 (m-10) REVERT: E 300 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: E 324 LYS cc_start: 0.8303 (mtmm) cc_final: 0.7885 (mtmm) REVERT: E 338 THR cc_start: 0.8633 (m) cc_final: 0.8294 (t) REVERT: E 340 LYS cc_start: 0.7671 (tttt) cc_final: 0.7366 (ttmt) REVERT: F 37 LYS cc_start: 0.7601 (mmtt) cc_final: 0.7294 (mmtm) REVERT: F 57 SER cc_start: 0.8547 (p) cc_final: 0.8295 (t) REVERT: F 60 ASN cc_start: 0.7952 (m-40) cc_final: 0.7656 (m-40) REVERT: F 69 ASP cc_start: 0.7227 (t70) cc_final: 0.6931 (t70) REVERT: F 75 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7664 (mmtp) REVERT: F 76 GLU cc_start: 0.6575 (tp30) cc_final: 0.6275 (tp30) REVERT: F 115 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7384 (mttm) REVERT: F 161 ARG cc_start: 0.7383 (mmm-85) cc_final: 0.7018 (mmm-85) REVERT: F 177 SER cc_start: 0.8839 (m) cc_final: 0.8445 (p) REVERT: F 261 LEU cc_start: 0.8510 (tp) cc_final: 0.8300 (mt) REVERT: F 290 LYS cc_start: 0.7693 (mttt) cc_final: 0.7455 (mttt) REVERT: H 38 ARG cc_start: 0.7252 (ptt-90) cc_final: 0.6896 (ptt-90) REVERT: H 40 SER cc_start: 0.8286 (p) cc_final: 0.7606 (t) REVERT: H 76 ASN cc_start: 0.6512 (p0) cc_final: 0.5724 (p0) REVERT: H 83 LYS cc_start: 0.8350 (tmtt) cc_final: 0.8022 (tptp) REVERT: L 20 THR cc_start: 0.8603 (t) cc_final: 0.8303 (p) REVERT: L 42 LYS cc_start: 0.8266 (mmmt) cc_final: 0.8029 (mmmt) REVERT: L 47 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7697 (mt) REVERT: L 90 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6394 (tm130) outliers start: 81 outliers final: 64 residues processed: 694 average time/residue: 0.3922 time to fit residues: 399.8028 Evaluate side-chains 720 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 649 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 166 LEU 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 307 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 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 66 GLN Chi-restraints excluded: chain C residue 79 LYS 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 220 VAL Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 288 THR 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 120 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 207 ILE 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 297 THR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 168 THR 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 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 48 GLN 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 273 GLU Chi-restraints excluded: chain F residue 277 THR 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 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 77 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 8 optimal weight: 0.0870 chunk 166 optimal weight: 0.0770 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 218 ASN C 270 ASN D 91 HIS ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 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 = 0.3461 r_free = 0.3461 target = 0.117327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104404 restraints weight = 30791.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107434 restraints weight = 13384.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109237 restraints weight = 7104.544| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19687 Z= 0.117 Angle : 0.623 8.823 26822 Z= 0.319 Chirality : 0.044 0.165 2935 Planarity : 0.004 0.048 3462 Dihedral : 5.014 25.435 2674 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 3.62 % Allowed : 19.47 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.17), residues: 2445 helix: -2.08 (0.65), residues: 49 sheet: -0.42 (0.17), residues: 882 loop : -1.63 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 330 HIS 0.006 0.001 HIS C 394 PHE 0.026 0.001 PHE C 356 TYR 0.035 0.001 TYR F 9 ARG 0.004 0.000 ARG D 103 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 493) hydrogen bonds : angle 5.05220 ( 1251) SS BOND : bond 0.00238 ( 40) SS BOND : angle 1.19368 ( 80) covalent geometry : bond 0.00273 (19647) covalent geometry : angle 0.62031 (26742) ********************** 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 755 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 679 time to evaluate : 2.571 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 9 SER cc_start: 0.7615 (t) cc_final: 0.7275 (t) REVERT: A 30 SER cc_start: 0.8069 (m) cc_final: 0.7686 (p) REVERT: A 35 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8078 (ttmm) REVERT: A 45 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6816 (mm-30) REVERT: A 52 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7944 (ttpp) REVERT: A 76 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6361 (tm-30) REVERT: A 105 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7704 (mtpp) REVERT: A 108 VAL cc_start: 0.8923 (t) cc_final: 0.8433 (m) REVERT: A 110 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8440 (mtmm) REVERT: A 111 SER cc_start: 0.8427 (p) cc_final: 0.8203 (t) REVERT: A 123 LYS cc_start: 0.7629 (mtmt) cc_final: 0.7397 (mtmt) REVERT: A 147 TYR cc_start: 0.7781 (m-10) cc_final: 0.7505 (m-10) REVERT: A 176 LYS cc_start: 0.8228 (mttt) cc_final: 0.7863 (mtpp) REVERT: A 205 SER cc_start: 0.8520 (t) cc_final: 0.8111 (p) REVERT: A 241 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6610 (tm-30) REVERT: A 245 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7288 (mtpp) REVERT: A 341 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 18 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7634 (ttt-90) REVERT: B 34 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 44 TYR cc_start: 0.8084 (m-80) cc_final: 0.7436 (m-80) REVERT: B 48 GLN cc_start: 0.7567 (tt0) cc_final: 0.7115 (tm-30) REVERT: B 62 LYS cc_start: 0.7461 (tttt) cc_final: 0.6951 (mtpp) REVERT: B 68 TYR cc_start: 0.8699 (p90) cc_final: 0.8469 (p90) REVERT: B 108 ASP cc_start: 0.7392 (p0) cc_final: 0.7029 (p0) REVERT: B 164 TYR cc_start: 0.8282 (m-80) cc_final: 0.7551 (m-80) REVERT: B 175 ASP cc_start: 0.6684 (t0) cc_final: 0.6331 (m-30) REVERT: B 227 ARG cc_start: 0.8324 (mmt-90) cc_final: 0.7909 (mpt180) REVERT: B 230 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8057 (ptp-110) REVERT: B 265 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7561 (mmtt) REVERT: B 283 VAL cc_start: 0.8293 (t) cc_final: 0.8002 (m) REVERT: B 294 TYR cc_start: 0.8288 (m-10) cc_final: 0.7448 (m-80) REVERT: B 324 LYS cc_start: 0.7585 (mtmm) cc_final: 0.7299 (mtmm) REVERT: B 336 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7840 (ttmm) REVERT: C 10 GLN cc_start: 0.7583 (tt0) cc_final: 0.7308 (tt0) REVERT: C 35 LYS cc_start: 0.8228 (tttt) cc_final: 0.7893 (tptp) REVERT: C 66 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6795 (mt0) REVERT: C 67 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6714 (mm-30) REVERT: C 104 SER cc_start: 0.7464 (m) cc_final: 0.7196 (t) REVERT: C 120 GLU cc_start: 0.7560 (pt0) cc_final: 0.6976 (pt0) REVERT: C 132 PHE cc_start: 0.7636 (m-10) cc_final: 0.7342 (m-10) REVERT: C 184 ILE cc_start: 0.8485 (mm) cc_final: 0.8008 (mt) REVERT: C 207 THR cc_start: 0.7969 (t) cc_final: 0.7691 (p) REVERT: C 214 TYR cc_start: 0.8444 (t80) cc_final: 0.7698 (t80) REVERT: C 218 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8321 (m-40) REVERT: C 222 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: C 266 ILE cc_start: 0.8419 (mt) cc_final: 0.8116 (mm) REVERT: C 288 THR cc_start: 0.6285 (OUTLIER) cc_final: 0.5922 (p) REVERT: C 338 THR cc_start: 0.8069 (m) cc_final: 0.7681 (t) REVERT: D 64 ARG cc_start: 0.7236 (mmm-85) cc_final: 0.6834 (mtp85) REVERT: D 74 ILE cc_start: 0.8161 (mt) cc_final: 0.7847 (mt) REVERT: D 130 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7649 (mtmm) REVERT: D 147 VAL cc_start: 0.8547 (p) cc_final: 0.8344 (m) REVERT: D 180 SER cc_start: 0.8367 (p) cc_final: 0.7838 (m) REVERT: D 215 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7454 (ttmm) REVERT: D 227 ARG cc_start: 0.7622 (ttm110) cc_final: 0.7325 (tpp80) REVERT: D 242 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7583 (mmtp) REVERT: D 257 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8634 (m) REVERT: D 330 TRP cc_start: 0.8753 (t-100) cc_final: 0.8390 (t-100) REVERT: D 336 LYS cc_start: 0.7829 (mttt) cc_final: 0.7612 (tttt) REVERT: D 354 GLU cc_start: 0.5159 (OUTLIER) cc_final: 0.2639 (tp30) REVERT: E 6 THR cc_start: 0.8099 (m) cc_final: 0.7780 (p) REVERT: E 87 PHE cc_start: 0.7878 (m-80) cc_final: 0.7538 (m-80) REVERT: E 161 ILE cc_start: 0.7625 (mt) cc_final: 0.7391 (mt) REVERT: E 188 ASP cc_start: 0.6885 (t70) cc_final: 0.6483 (t70) REVERT: E 202 ASP cc_start: 0.8181 (p0) cc_final: 0.7973 (p0) REVERT: E 203 ILE cc_start: 0.8081 (mm) cc_final: 0.7832 (pt) REVERT: E 222 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7646 (mt0) REVERT: E 246 ASP cc_start: 0.7037 (m-30) cc_final: 0.6736 (m-30) REVERT: E 280 PHE cc_start: 0.8448 (m-10) cc_final: 0.7978 (m-10) REVERT: E 324 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7906 (mtmm) REVERT: E 338 THR cc_start: 0.8639 (m) cc_final: 0.8325 (t) REVERT: E 340 LYS cc_start: 0.7671 (tttt) cc_final: 0.7353 (ttmt) REVERT: F 37 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7302 (mmtm) REVERT: F 57 SER cc_start: 0.8541 (p) cc_final: 0.8299 (t) REVERT: F 60 ASN cc_start: 0.7975 (m-40) cc_final: 0.7645 (m-40) REVERT: F 69 ASP cc_start: 0.7127 (t70) cc_final: 0.6868 (t70) REVERT: F 75 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7720 (mmtp) REVERT: F 76 GLU cc_start: 0.6557 (tp30) cc_final: 0.6257 (tp30) REVERT: F 115 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7361 (mttm) REVERT: F 161 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.6993 (mmm-85) REVERT: F 177 SER cc_start: 0.8847 (m) cc_final: 0.8483 (p) REVERT: F 227 ARG cc_start: 0.7172 (mmt-90) cc_final: 0.6913 (mtt90) REVERT: F 261 LEU cc_start: 0.8512 (tp) cc_final: 0.8304 (mt) REVERT: F 290 LYS cc_start: 0.7687 (mttt) cc_final: 0.7446 (mttt) REVERT: H 38 ARG cc_start: 0.7251 (ptt-90) cc_final: 0.6892 (ptt-90) REVERT: H 40 SER cc_start: 0.8117 (p) cc_final: 0.7478 (t) REVERT: H 76 ASN cc_start: 0.6508 (p0) cc_final: 0.5727 (p0) REVERT: H 83 LYS cc_start: 0.8353 (tmtt) cc_final: 0.8025 (tptp) REVERT: L 20 THR cc_start: 0.8590 (t) cc_final: 0.8283 (p) REVERT: L 42 LYS cc_start: 0.8258 (mmmt) cc_final: 0.8014 (mmmt) REVERT: L 47 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7675 (mt) REVERT: L 90 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6406 (tm130) outliers start: 76 outliers final: 57 residues processed: 712 average time/residue: 0.4376 time to fit residues: 457.4794 Evaluate side-chains 733 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 667 time to evaluate : 2.288 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 166 LEU 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 307 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 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 66 GLN Chi-restraints excluded: chain C residue 79 LYS 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 220 VAL Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 288 THR 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 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 242 LYS Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 183 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 E residue 392 GLN Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 277 THR 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 47 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 99 optimal weight: 0.0670 chunk 200 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN C 218 ASN C 270 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103179 restraints weight = 30897.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106222 restraints weight = 13491.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108033 restraints weight = 7178.527| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19687 Z= 0.138 Angle : 0.633 8.993 26822 Z= 0.324 Chirality : 0.045 0.166 2935 Planarity : 0.004 0.046 3462 Dihedral : 5.038 25.012 2674 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 3.62 % Allowed : 19.85 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2445 helix: -1.98 (0.66), residues: 49 sheet: -0.39 (0.17), residues: 883 loop : -1.59 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.006 0.001 HIS C 394 PHE 0.025 0.001 PHE C 356 TYR 0.033 0.001 TYR F 9 ARG 0.004 0.000 ARG D 103 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 493) hydrogen bonds : angle 5.07237 ( 1251) SS BOND : bond 0.00263 ( 40) SS BOND : angle 1.22707 ( 80) covalent geometry : bond 0.00322 (19647) covalent geometry : angle 0.63064 (26742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8915.77 seconds wall clock time: 159 minutes 42.65 seconds (9582.65 seconds total)