Starting phenix.real_space_refine on Sat Sep 28 10:49:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/09_2024/8eeu_28058.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/09_2024/8eeu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/09_2024/8eeu_28058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/09_2024/8eeu_28058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/09_2024/8eeu_28058.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/09_2024/8eeu_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-5461/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: 11.03, per 1000 atoms: 0.58 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 2.3 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: 2.70 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: 5.97 Time building geometry restraints manager: 5.06 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 41.200 Find NCS groups from input model: 0.910 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.810 ------------------------------------------------------------------------------- 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 19647 Z= 0.772 Angle : 0.935 8.408 26742 Z= 0.519 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 824 time to evaluate : 2.313 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: 0.3577 time to fit residues: 431.2298 Evaluate side-chains 714 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 713 time to evaluate : 2.049 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19647 Z= 0.206 Angle : 0.639 8.578 26742 Z= 0.337 Chirality : 0.046 0.208 2935 Planarity : 0.006 0.049 3462 Dihedral : 5.879 29.916 2676 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.91 % Favored : 93.05 % Rotamer: Outliers : 1.33 % Allowed : 8.81 % Favored : 89.86 % 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: -3.65 (0.15), residues: 2445 helix: -3.46 (0.45), residues: 54 sheet: -1.90 (0.15), residues: 944 loop : -2.85 (0.14), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 170 HIS 0.008 0.001 HIS C 394 PHE 0.020 0.002 PHE C 287 TYR 0.027 0.001 TYR A 122 ARG 0.005 0.001 ARG D 21 *********************** 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 759 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 731 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 SER cc_start: 0.7724 (t) cc_final: 0.7429 (t) REVERT: A 29 ILE cc_start: 0.8591 (mt) cc_final: 0.8363 (mp) REVERT: A 30 SER cc_start: 0.8300 (m) cc_final: 0.7624 (p) REVERT: A 35 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7570 (ttmm) REVERT: A 37 LYS cc_start: 0.8200 (mttt) cc_final: 0.7940 (mtmm) REVERT: A 42 VAL cc_start: 0.8341 (t) cc_final: 0.7860 (m) REVERT: A 45 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6798 (mm-30) REVERT: A 52 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8000 (ttpp) REVERT: A 76 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6205 (tm-30) REVERT: A 82 THR cc_start: 0.7602 (m) cc_final: 0.7351 (p) REVERT: A 105 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7740 (mtpp) REVERT: A 111 SER cc_start: 0.7960 (t) cc_final: 0.7397 (t) REVERT: A 123 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7313 (mtmt) REVERT: A 130 GLN cc_start: 0.7548 (tt0) cc_final: 0.7173 (tt0) REVERT: A 137 VAL cc_start: 0.8132 (t) cc_final: 0.7740 (p) REVERT: A 147 TYR cc_start: 0.7639 (m-10) cc_final: 0.7205 (m-80) REVERT: A 176 LYS cc_start: 0.8225 (mttt) cc_final: 0.7817 (mtpp) REVERT: A 183 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6311 (mt-10) REVERT: A 205 SER cc_start: 0.8533 (t) cc_final: 0.8049 (p) REVERT: A 252 LYS cc_start: 0.8754 (tttt) cc_final: 0.8476 (ttmm) REVERT: A 269 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6656 (mt-10) REVERT: A 281 ASP cc_start: 0.7831 (t0) cc_final: 0.7479 (t0) REVERT: A 284 ASP cc_start: 0.7044 (m-30) cc_final: 0.6806 (m-30) REVERT: A 291 SER cc_start: 0.8303 (p) cc_final: 0.8075 (t) REVERT: A 300 GLU cc_start: 0.7243 (pt0) cc_final: 0.6948 (pt0) REVERT: A 307 VAL cc_start: 0.8709 (t) cc_final: 0.8439 (p) REVERT: A 341 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7267 (mm-30) REVERT: A 345 GLU cc_start: 0.7436 (mp0) cc_final: 0.7218 (mp0) REVERT: A 368 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6848 (tm-30) REVERT: A 377 LYS cc_start: 0.7711 (mttp) cc_final: 0.7492 (mttp) REVERT: B 34 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 37 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7286 (mttt) REVERT: B 66 MET cc_start: 0.8458 (ttp) cc_final: 0.8254 (ttm) REVERT: B 68 TYR cc_start: 0.8631 (p90) cc_final: 0.8310 (p90) REVERT: B 108 ASP cc_start: 0.7427 (p0) cc_final: 0.7014 (p0) REVERT: B 115 LYS cc_start: 0.7528 (mtpt) cc_final: 0.7295 (mtpp) REVERT: B 164 TYR cc_start: 0.8024 (m-80) cc_final: 0.7473 (m-80) REVERT: B 175 ASP cc_start: 0.6828 (t0) cc_final: 0.6538 (t0) REVERT: B 192 ASP cc_start: 0.7087 (t70) cc_final: 0.6868 (t70) REVERT: B 294 TYR cc_start: 0.7598 (m-10) cc_final: 0.7204 (m-10) REVERT: B 324 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7414 (mtmm) REVERT: B 336 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7839 (ttmm) REVERT: C 26 PRO cc_start: 0.7862 (Cg_exo) cc_final: 0.7622 (Cg_endo) REVERT: C 104 SER cc_start: 0.7932 (m) cc_final: 0.7676 (t) REVERT: C 107 TYR cc_start: 0.7815 (p90) cc_final: 0.7581 (p90) REVERT: C 117 ASP cc_start: 0.7607 (t70) cc_final: 0.7300 (t70) REVERT: C 120 GLU cc_start: 0.7653 (pt0) cc_final: 0.7179 (pt0) REVERT: C 186 ASN cc_start: 0.8042 (m110) cc_final: 0.7718 (m110) REVERT: C 245 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7463 (mtpt) REVERT: C 246 ASP cc_start: 0.6842 (m-30) cc_final: 0.6528 (m-30) REVERT: C 254 THR cc_start: 0.8380 (p) cc_final: 0.8135 (t) REVERT: C 261 ILE cc_start: 0.8036 (mm) cc_final: 0.7611 (mm) REVERT: C 334 SER cc_start: 0.8534 (t) cc_final: 0.8083 (p) REVERT: C 392 GLN cc_start: 0.7830 (mt0) cc_final: 0.7591 (mt0) REVERT: D 31 ILE cc_start: 0.8033 (tt) cc_final: 0.7705 (tt) REVERT: D 34 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7305 (mm-30) REVERT: D 61 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7905 (mp) REVERT: D 64 ARG cc_start: 0.7230 (mmm-85) cc_final: 0.6894 (mtp85) REVERT: D 74 ILE cc_start: 0.8165 (mt) cc_final: 0.7915 (mt) REVERT: D 75 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8125 (mttm) REVERT: D 77 ILE cc_start: 0.8337 (mt) cc_final: 0.7931 (tt) REVERT: D 82 VAL cc_start: 0.8627 (t) cc_final: 0.8328 (p) REVERT: D 94 ASP cc_start: 0.6947 (t0) cc_final: 0.6683 (t0) REVERT: D 111 THR cc_start: 0.7874 (m) cc_final: 0.7672 (m) REVERT: D 122 SER cc_start: 0.8456 (t) cc_final: 0.8182 (m) REVERT: D 130 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7405 (mtmm) REVERT: D 134 VAL cc_start: 0.8551 (t) cc_final: 0.8301 (t) REVERT: D 176 SER cc_start: 0.7838 (p) cc_final: 0.7574 (t) REVERT: D 180 SER cc_start: 0.7809 (p) cc_final: 0.7406 (m) REVERT: D 215 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7553 (ttmm) REVERT: D 242 LYS cc_start: 0.8075 (mttm) cc_final: 0.7622 (mttp) REVERT: D 254 LYS cc_start: 0.8502 (mtmp) cc_final: 0.8179 (mtpp) REVERT: D 277 THR cc_start: 0.8237 (m) cc_final: 0.7839 (p) REVERT: D 338 PHE cc_start: 0.8150 (m-10) cc_final: 0.7813 (m-80) REVERT: E 6 THR cc_start: 0.8102 (m) cc_final: 0.7712 (p) REVERT: E 9 SER cc_start: 0.8455 (t) cc_final: 0.8160 (t) REVERT: E 15 TYR cc_start: 0.7260 (t80) cc_final: 0.6969 (t80) REVERT: E 18 ILE cc_start: 0.8592 (pt) cc_final: 0.8379 (mt) REVERT: E 27 LEU cc_start: 0.8495 (tp) cc_final: 0.8205 (tt) REVERT: E 35 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7640 (mtpp) REVERT: E 47 VAL cc_start: 0.8311 (m) cc_final: 0.7976 (p) REVERT: E 79 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7564 (ttmm) REVERT: E 157 ASN cc_start: 0.7745 (t0) cc_final: 0.7521 (t0) REVERT: E 188 ASP cc_start: 0.6985 (t70) cc_final: 0.6609 (t70) REVERT: E 202 ASP cc_start: 0.7967 (p0) cc_final: 0.7731 (p0) REVERT: E 222 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7645 (mt0) REVERT: E 246 ASP cc_start: 0.7104 (m-30) cc_final: 0.6737 (m-30) REVERT: E 252 LYS cc_start: 0.8027 (tttt) cc_final: 0.7722 (ptmm) REVERT: E 269 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7139 (mt-10) REVERT: E 300 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6871 (tm-30) REVERT: E 304 ASN cc_start: 0.8001 (m110) cc_final: 0.7571 (m-40) REVERT: E 324 LYS cc_start: 0.8237 (mtmp) cc_final: 0.7980 (mtmm) REVERT: E 338 THR cc_start: 0.8284 (m) cc_final: 0.8001 (t) REVERT: E 340 LYS cc_start: 0.7616 (tttt) cc_final: 0.7320 (ttmt) REVERT: F 8 GLU cc_start: 0.7389 (tp30) cc_final: 0.7096 (tp30) REVERT: F 12 THR cc_start: 0.8030 (m) cc_final: 0.7582 (t) REVERT: F 37 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7200 (mmtm) REVERT: F 53 TYR cc_start: 0.8217 (m-80) cc_final: 0.7716 (m-80) REVERT: F 57 SER cc_start: 0.8478 (p) cc_final: 0.8218 (t) REVERT: F 60 ASN cc_start: 0.7956 (m-40) cc_final: 0.7599 (m-40) REVERT: F 75 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7812 (mmtp) REVERT: F 100 LEU cc_start: 0.8025 (tp) cc_final: 0.7823 (tt) REVERT: F 120 ARG cc_start: 0.7279 (ptp-110) cc_final: 0.7078 (ttm-80) REVERT: F 144 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6618 (mt-10) REVERT: F 175 ASP cc_start: 0.8277 (t0) cc_final: 0.7895 (t0) REVERT: F 177 SER cc_start: 0.8665 (m) cc_final: 0.8332 (p) REVERT: F 215 LYS cc_start: 0.7965 (tttt) cc_final: 0.7677 (tttt) REVERT: F 290 LYS cc_start: 0.7579 (mttt) cc_final: 0.7336 (mttt) REVERT: F 347 ASN cc_start: 0.8281 (t0) cc_final: 0.7987 (t0) REVERT: H 39 GLN cc_start: 0.8317 (tt0) cc_final: 0.7896 (tt0) REVERT: H 85 GLU cc_start: 0.7921 (tp30) cc_final: 0.7613 (tp30) REVERT: L 20 THR cc_start: 0.8628 (t) cc_final: 0.8361 (p) REVERT: L 42 LYS cc_start: 0.8217 (mmmt) cc_final: 0.7960 (mmmt) REVERT: L 104 VAL cc_start: 0.7892 (t) cc_final: 0.7549 (p) outliers start: 28 outliers final: 19 residues processed: 746 average time/residue: 0.3350 time to fit residues: 364.0200 Evaluate side-chains 724 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 704 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 61 LEU 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 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 238 optimal weight: 0.0270 chunk 196 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 179 GLN A 235 GLN A 270 ASN B 288 HIS B 333 HIS ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS D 71 HIS D 160 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19647 Z= 0.281 Angle : 0.634 7.965 26742 Z= 0.332 Chirality : 0.046 0.165 2935 Planarity : 0.005 0.045 3462 Dihedral : 5.627 28.404 2674 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 3.24 % Allowed : 11.85 % Favored : 84.91 % 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: -2.91 (0.16), residues: 2445 helix: -2.62 (0.59), residues: 48 sheet: -1.34 (0.17), residues: 915 loop : -2.39 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 103 HIS 0.006 0.001 HIS C 394 PHE 0.023 0.002 PHE C 356 TYR 0.049 0.002 TYR F 9 ARG 0.007 0.001 ARG E 73 *********************** 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 784 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 716 time to evaluate : 2.119 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: 0.7766 (t) cc_final: 0.7446 (t) REVERT: A 18 ILE cc_start: 0.8266 (pt) cc_final: 0.8031 (mm) REVERT: A 30 SER cc_start: 0.8198 (m) cc_final: 0.7680 (p) REVERT: A 35 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7430 (ttmm) REVERT: A 37 LYS cc_start: 0.8241 (mttt) cc_final: 0.7620 (mtmm) REVERT: A 42 VAL cc_start: 0.8633 (t) cc_final: 0.8163 (m) REVERT: A 45 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6927 (mm-30) REVERT: A 52 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8108 (ttpp) REVERT: A 75 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: A 76 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6245 (tm-30) REVERT: A 105 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7740 (mtpp) REVERT: A 108 VAL cc_start: 0.8828 (t) cc_final: 0.8288 (m) REVERT: A 111 SER cc_start: 0.8180 (t) cc_final: 0.7763 (t) REVERT: A 123 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7415 (mtmt) REVERT: A 130 GLN cc_start: 0.7533 (tt0) cc_final: 0.7288 (tt0) REVERT: A 147 TYR cc_start: 0.7702 (m-10) cc_final: 0.7229 (m-10) REVERT: A 176 LYS cc_start: 0.8315 (mttt) cc_final: 0.7965 (mtpp) REVERT: A 183 GLU cc_start: 0.6559 (mt-10) cc_final: 0.6295 (mt-10) REVERT: A 205 SER cc_start: 0.8489 (t) cc_final: 0.8045 (p) REVERT: A 241 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 252 LYS cc_start: 0.8769 (tttt) cc_final: 0.8514 (ttmm) REVERT: A 269 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 281 ASP cc_start: 0.7827 (t0) cc_final: 0.7515 (t0) REVERT: A 307 VAL cc_start: 0.8721 (t) cc_final: 0.8459 (p) REVERT: A 344 VAL cc_start: 0.8367 (m) cc_final: 0.8046 (p) REVERT: A 368 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6944 (tm-30) REVERT: B 34 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7093 (mm-30) REVERT: B 37 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7254 (mmtt) REVERT: B 62 LYS cc_start: 0.7409 (tttt) cc_final: 0.6826 (mtpp) REVERT: B 108 ASP cc_start: 0.7432 (p0) cc_final: 0.7023 (p0) REVERT: B 159 GLN cc_start: 0.7965 (mt0) cc_final: 0.7702 (mt0) REVERT: B 164 TYR cc_start: 0.8116 (m-80) cc_final: 0.7477 (m-80) REVERT: B 254 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7269 (mmmt) REVERT: B 294 TYR cc_start: 0.7984 (m-10) cc_final: 0.7591 (m-80) REVERT: B 324 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7464 (mtmm) REVERT: B 336 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7885 (ttmm) REVERT: C 10 GLN cc_start: 0.7651 (tt0) cc_final: 0.7365 (tt0) REVERT: C 35 LYS cc_start: 0.8367 (tttt) cc_final: 0.7834 (tttm) REVERT: C 37 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7288 (ttmm) REVERT: C 120 GLU cc_start: 0.7725 (pt0) cc_final: 0.7519 (pt0) REVERT: C 132 PHE cc_start: 0.7674 (m-10) cc_final: 0.7445 (m-10) REVERT: C 186 ASN cc_start: 0.8236 (m110) cc_final: 0.7908 (m110) REVERT: C 207 THR cc_start: 0.7956 (t) cc_final: 0.7681 (p) REVERT: C 242 GLN cc_start: 0.7611 (tp40) cc_final: 0.7106 (tp-100) REVERT: C 245 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7544 (mtpt) REVERT: C 246 ASP cc_start: 0.6863 (m-30) cc_final: 0.6550 (m-30) REVERT: C 254 THR cc_start: 0.8506 (p) cc_final: 0.8222 (t) REVERT: C 260 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6763 (mt-10) REVERT: C 261 ILE cc_start: 0.8320 (mm) cc_final: 0.7916 (mm) REVERT: C 334 SER cc_start: 0.8543 (t) cc_final: 0.8062 (p) REVERT: C 338 THR cc_start: 0.7934 (m) cc_final: 0.7492 (t) REVERT: C 362 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.7200 (m170) REVERT: C 379 ASP cc_start: 0.6880 (t0) cc_final: 0.6661 (t0) REVERT: D 34 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7289 (mm-30) REVERT: D 64 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.6904 (mtt-85) REVERT: D 74 ILE cc_start: 0.8184 (mt) cc_final: 0.7935 (mt) REVERT: D 75 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8049 (mttm) REVERT: D 77 ILE cc_start: 0.8415 (mt) cc_final: 0.8083 (tt) REVERT: D 94 ASP cc_start: 0.6866 (t0) cc_final: 0.6571 (t0) REVERT: D 130 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7486 (mtmm) REVERT: D 134 VAL cc_start: 0.8590 (t) cc_final: 0.8346 (t) REVERT: D 176 SER cc_start: 0.7885 (p) cc_final: 0.7682 (t) REVERT: D 180 SER cc_start: 0.8018 (p) cc_final: 0.7617 (m) REVERT: D 215 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7531 (ttmm) REVERT: D 241 ASP cc_start: 0.7835 (p0) cc_final: 0.7475 (p0) REVERT: D 242 LYS cc_start: 0.8174 (mttm) cc_final: 0.7781 (mttp) REVERT: D 254 LYS cc_start: 0.8590 (mtmp) cc_final: 0.8166 (mtpp) REVERT: D 277 THR cc_start: 0.8283 (m) cc_final: 0.7860 (p) REVERT: D 316 VAL cc_start: 0.8701 (t) cc_final: 0.8438 (p) REVERT: D 338 PHE cc_start: 0.8130 (m-10) cc_final: 0.7873 (m-80) REVERT: E 6 THR cc_start: 0.8196 (m) cc_final: 0.7788 (p) REVERT: E 15 TYR cc_start: 0.7322 (t80) cc_final: 0.7068 (t80) REVERT: E 35 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7660 (mtpp) REVERT: E 47 VAL cc_start: 0.8312 (m) cc_final: 0.8012 (p) REVERT: E 77 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7431 (mm-40) REVERT: E 110 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8212 (mtmm) REVERT: E 157 ASN cc_start: 0.7769 (t0) cc_final: 0.7449 (t0) REVERT: E 188 ASP cc_start: 0.7017 (t70) cc_final: 0.6618 (t70) REVERT: E 202 ASP cc_start: 0.8177 (p0) cc_final: 0.7913 (p0) REVERT: E 222 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7703 (mt0) REVERT: E 246 ASP cc_start: 0.7137 (m-30) cc_final: 0.6782 (m-30) REVERT: E 252 LYS cc_start: 0.8148 (tttt) cc_final: 0.7909 (tttt) REVERT: E 262 TYR cc_start: 0.7557 (m-80) cc_final: 0.6343 (m-80) REVERT: E 269 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7182 (mt-10) REVERT: E 280 PHE cc_start: 0.8439 (m-10) cc_final: 0.7982 (m-10) REVERT: E 300 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6813 (tm-30) REVERT: E 304 ASN cc_start: 0.8024 (m110) cc_final: 0.7653 (m-40) REVERT: E 324 LYS cc_start: 0.8262 (mtmp) cc_final: 0.8044 (mtmm) REVERT: E 336 THR cc_start: 0.7155 (m) cc_final: 0.6939 (m) REVERT: E 338 THR cc_start: 0.8499 (m) cc_final: 0.8207 (t) REVERT: E 340 LYS cc_start: 0.7750 (tttt) cc_final: 0.7430 (ttmt) REVERT: F 8 GLU cc_start: 0.7417 (tp30) cc_final: 0.7117 (tp30) REVERT: F 16 MET cc_start: 0.7940 (mtp) cc_final: 0.7690 (mtp) REVERT: F 19 CYS cc_start: 0.6825 (t) cc_final: 0.6588 (t) REVERT: F 34 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: F 53 TYR cc_start: 0.8233 (m-80) cc_final: 0.7769 (m-80) REVERT: F 57 SER cc_start: 0.8523 (p) cc_final: 0.7993 (t) REVERT: F 60 ASN cc_start: 0.8079 (m-40) cc_final: 0.7717 (m-40) REVERT: F 69 ASP cc_start: 0.7414 (t70) cc_final: 0.7168 (t70) REVERT: F 75 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7377 (mmtp) REVERT: F 76 GLU cc_start: 0.6624 (tp30) cc_final: 0.6170 (tp30) REVERT: F 120 ARG cc_start: 0.7375 (ptp-110) cc_final: 0.7122 (ttp80) REVERT: F 129 VAL cc_start: 0.8136 (t) cc_final: 0.7764 (p) REVERT: F 175 ASP cc_start: 0.8369 (t0) cc_final: 0.7933 (t0) REVERT: F 177 SER cc_start: 0.8670 (m) cc_final: 0.8389 (p) REVERT: F 241 ASP cc_start: 0.7676 (p0) cc_final: 0.7459 (p0) REVERT: F 245 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7891 (ptmt) REVERT: F 261 LEU cc_start: 0.8562 (tp) cc_final: 0.8283 (mt) REVERT: F 290 LYS cc_start: 0.7779 (mttt) cc_final: 0.7491 (mttt) REVERT: F 347 ASN cc_start: 0.8414 (t0) cc_final: 0.8106 (t0) REVERT: H 38 ARG cc_start: 0.7108 (ptt-90) cc_final: 0.6833 (ptt-90) REVERT: H 76 ASN cc_start: 0.6442 (p0) cc_final: 0.5784 (p0) REVERT: L 20 THR cc_start: 0.8662 (t) cc_final: 0.8369 (p) REVERT: L 42 LYS cc_start: 0.8294 (mmmt) cc_final: 0.8027 (mmmt) REVERT: L 47 LEU cc_start: 0.8206 (mp) cc_final: 0.8004 (mm) REVERT: L 54 LEU cc_start: 0.8700 (tp) cc_final: 0.8408 (tp) REVERT: L 104 VAL cc_start: 0.7993 (t) cc_final: 0.7752 (p) outliers start: 68 outliers final: 44 residues processed: 743 average time/residue: 0.3370 time to fit residues: 365.6821 Evaluate side-chains 742 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 695 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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 73 THR 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 220 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 269 GLU 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 50 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 270 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 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 325 SER 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 119 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain L residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 114 optimal weight: 0.0020 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 234 optimal weight: 0.0970 chunk 115 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN E 360 ASN F 52 GLN F 81 GLN F 132 ASN F 288 HIS F 305 HIS F 318 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19647 Z= 0.188 Angle : 0.598 8.578 26742 Z= 0.309 Chirality : 0.044 0.166 2935 Planarity : 0.004 0.043 3462 Dihedral : 5.296 27.039 2674 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 3.19 % Allowed : 14.14 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.11 (0.65), residues: 48 sheet: -1.04 (0.17), residues: 917 loop : -2.14 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.015 0.001 HIS C 362 PHE 0.017 0.001 PHE C 156 TYR 0.045 0.001 TYR F 9 ARG 0.005 0.000 ARG D 227 *********************** 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 766 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 699 time to evaluate : 3.452 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: 0.7777 (t) cc_final: 0.7443 (t) REVERT: A 18 ILE cc_start: 0.8046 (pt) cc_final: 0.7808 (mm) REVERT: A 30 SER cc_start: 0.8125 (m) cc_final: 0.7642 (p) REVERT: A 35 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7536 (ttmm) REVERT: A 37 LYS cc_start: 0.8220 (mttt) cc_final: 0.7666 (mtmm) REVERT: A 42 VAL cc_start: 0.8496 (t) cc_final: 0.7976 (m) REVERT: A 45 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6880 (mm-30) REVERT: A 52 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8111 (ttpp) REVERT: A 76 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6290 (tm-30) REVERT: A 82 THR cc_start: 0.7622 (m) cc_final: 0.7334 (p) REVERT: A 105 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7715 (mtpp) REVERT: A 108 VAL cc_start: 0.8842 (t) cc_final: 0.8331 (m) REVERT: A 111 SER cc_start: 0.8188 (t) cc_final: 0.7778 (t) REVERT: A 123 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7310 (mtmt) REVERT: A 130 GLN cc_start: 0.7534 (tt0) cc_final: 0.6946 (tt0) REVERT: A 147 TYR cc_start: 0.7747 (m-10) cc_final: 0.7126 (m-80) REVERT: A 176 LYS cc_start: 0.8321 (mttt) cc_final: 0.7959 (mtpp) REVERT: A 183 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6276 (mt-10) REVERT: A 205 SER cc_start: 0.8463 (t) cc_final: 0.8052 (p) REVERT: A 241 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 252 LYS cc_start: 0.8748 (tttt) cc_final: 0.8485 (ttmm) REVERT: A 269 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6598 (mt-10) REVERT: A 281 ASP cc_start: 0.7769 (t0) cc_final: 0.7442 (t0) REVERT: A 307 VAL cc_start: 0.8705 (t) cc_final: 0.8442 (p) REVERT: A 368 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6866 (tm-30) REVERT: B 34 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 37 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7132 (mmtt) REVERT: B 68 TYR cc_start: 0.8624 (p90) cc_final: 0.8349 (p90) REVERT: B 108 ASP cc_start: 0.7471 (p0) cc_final: 0.7062 (p0) REVERT: B 159 GLN cc_start: 0.7971 (mt0) cc_final: 0.7725 (mt0) REVERT: B 164 TYR cc_start: 0.8099 (m-80) cc_final: 0.7460 (m-80) REVERT: B 230 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8012 (ptp-110) REVERT: B 254 LYS cc_start: 0.7437 (mmmt) cc_final: 0.7212 (mmmt) REVERT: B 265 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7371 (mmmm) REVERT: B 294 TYR cc_start: 0.7960 (m-10) cc_final: 0.7654 (m-10) REVERT: B 324 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7387 (mtmm) REVERT: B 336 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7867 (ttmm) REVERT: C 10 GLN cc_start: 0.7637 (tt0) cc_final: 0.7347 (tt0) REVERT: C 37 LYS cc_start: 0.7587 (ttmt) cc_final: 0.7075 (mtpt) REVERT: C 107 TYR cc_start: 0.7901 (p90) cc_final: 0.7231 (p90) REVERT: C 132 PHE cc_start: 0.7702 (m-10) cc_final: 0.7222 (m-10) REVERT: C 145 THR cc_start: 0.8242 (m) cc_final: 0.7640 (p) REVERT: C 186 ASN cc_start: 0.8247 (m110) cc_final: 0.7974 (m110) REVERT: C 207 THR cc_start: 0.7978 (t) cc_final: 0.7661 (p) REVERT: C 222 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7447 (mt0) REVERT: C 242 GLN cc_start: 0.7636 (tp40) cc_final: 0.7037 (tp-100) REVERT: C 245 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7521 (mtpt) REVERT: C 246 ASP cc_start: 0.6885 (m-30) cc_final: 0.6553 (m-30) REVERT: C 254 THR cc_start: 0.8463 (p) cc_final: 0.8189 (t) REVERT: C 260 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6661 (mt-10) REVERT: C 261 ILE cc_start: 0.8319 (mm) cc_final: 0.7917 (mm) REVERT: C 334 SER cc_start: 0.8471 (t) cc_final: 0.7980 (p) REVERT: C 338 THR cc_start: 0.7947 (m) cc_final: 0.7521 (t) REVERT: D 34 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7197 (mm-30) REVERT: D 64 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.6908 (mtt-85) REVERT: D 74 ILE cc_start: 0.8235 (mt) cc_final: 0.7940 (mt) REVERT: D 75 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8175 (mttm) REVERT: D 77 ILE cc_start: 0.8312 (mt) cc_final: 0.8101 (tt) REVERT: D 94 ASP cc_start: 0.6888 (t0) cc_final: 0.6637 (t0) REVERT: D 130 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7486 (mtmm) REVERT: D 180 SER cc_start: 0.8175 (p) cc_final: 0.7738 (m) REVERT: D 215 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7488 (ttmm) REVERT: D 227 ARG cc_start: 0.7469 (ttm110) cc_final: 0.6978 (ttm110) REVERT: D 241 ASP cc_start: 0.7841 (p0) cc_final: 0.7435 (p0) REVERT: D 242 LYS cc_start: 0.8172 (mttm) cc_final: 0.7820 (mttp) REVERT: D 254 LYS cc_start: 0.8593 (mtmp) cc_final: 0.8193 (mtpp) REVERT: D 277 THR cc_start: 0.8305 (m) cc_final: 0.7868 (p) REVERT: D 338 PHE cc_start: 0.8091 (m-10) cc_final: 0.7865 (m-80) REVERT: E 6 THR cc_start: 0.8180 (m) cc_final: 0.7759 (p) REVERT: E 15 TYR cc_start: 0.7277 (t80) cc_final: 0.7042 (t80) REVERT: E 35 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7674 (mtpp) REVERT: E 47 VAL cc_start: 0.8334 (m) cc_final: 0.8023 (p) REVERT: E 110 LYS cc_start: 0.8513 (ptpp) cc_final: 0.8157 (mtmm) REVERT: E 157 ASN cc_start: 0.7757 (t0) cc_final: 0.7384 (t0) REVERT: E 188 ASP cc_start: 0.7014 (t70) cc_final: 0.6579 (t70) REVERT: E 202 ASP cc_start: 0.8143 (p0) cc_final: 0.7830 (p0) REVERT: E 203 ILE cc_start: 0.8072 (mm) cc_final: 0.7470 (tt) REVERT: E 222 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7635 (mt0) REVERT: E 245 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7476 (mtpp) REVERT: E 246 ASP cc_start: 0.7143 (m-30) cc_final: 0.6730 (m-30) REVERT: E 252 LYS cc_start: 0.8177 (tttt) cc_final: 0.7963 (tttt) REVERT: E 253 PHE cc_start: 0.7687 (m-10) cc_final: 0.7474 (m-80) REVERT: E 262 TYR cc_start: 0.7657 (m-80) cc_final: 0.6258 (m-80) REVERT: E 269 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7136 (mt-10) REVERT: E 280 PHE cc_start: 0.8447 (m-10) cc_final: 0.7994 (m-10) REVERT: E 300 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6809 (tm-30) REVERT: E 324 LYS cc_start: 0.8313 (mtmp) cc_final: 0.8104 (mtmm) REVERT: E 338 THR cc_start: 0.8462 (m) cc_final: 0.8139 (t) REVERT: E 340 LYS cc_start: 0.7688 (tttt) cc_final: 0.7400 (ttmt) REVERT: F 8 GLU cc_start: 0.7375 (tp30) cc_final: 0.7101 (tp30) REVERT: F 16 MET cc_start: 0.7949 (mtp) cc_final: 0.7701 (mtp) REVERT: F 53 TYR cc_start: 0.8191 (m-80) cc_final: 0.7851 (m-80) REVERT: F 57 SER cc_start: 0.8570 (p) cc_final: 0.8259 (t) REVERT: F 60 ASN cc_start: 0.7955 (m-40) cc_final: 0.7632 (m-40) REVERT: F 69 ASP cc_start: 0.7339 (t70) cc_final: 0.7101 (t70) REVERT: F 75 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7802 (mmtp) REVERT: F 120 ARG cc_start: 0.7388 (ptp-110) cc_final: 0.7134 (ttp80) REVERT: F 175 ASP cc_start: 0.8385 (t0) cc_final: 0.7918 (t0) REVERT: F 177 SER cc_start: 0.8698 (m) cc_final: 0.8395 (p) REVERT: F 227 ARG cc_start: 0.7281 (tpp80) cc_final: 0.6993 (mmt-90) REVERT: F 241 ASP cc_start: 0.7599 (p0) cc_final: 0.7358 (p0) REVERT: F 245 LYS cc_start: 0.8175 (ptmt) cc_final: 0.7794 (ttpt) REVERT: F 261 LEU cc_start: 0.8541 (tp) cc_final: 0.8297 (mt) REVERT: F 286 LYS cc_start: 0.8268 (tppp) cc_final: 0.7902 (tppp) REVERT: F 290 LYS cc_start: 0.7752 (mttt) cc_final: 0.7454 (mttt) REVERT: H 38 ARG cc_start: 0.7173 (ptt-90) cc_final: 0.6752 (ptt-90) REVERT: H 76 ASN cc_start: 0.6323 (p0) cc_final: 0.5523 (p0) REVERT: L 20 THR cc_start: 0.8602 (t) cc_final: 0.8330 (p) REVERT: L 42 LYS cc_start: 0.8279 (mmmt) cc_final: 0.8013 (mmmt) REVERT: L 47 LEU cc_start: 0.8175 (mp) cc_final: 0.7962 (mp) REVERT: L 54 LEU cc_start: 0.8698 (tp) cc_final: 0.8415 (tp) REVERT: L 104 VAL cc_start: 0.7994 (t) cc_final: 0.7775 (p) outliers start: 67 outliers final: 44 residues processed: 727 average time/residue: 0.3508 time to fit residues: 373.0388 Evaluate side-chains 721 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 675 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 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 33 ILE 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 218 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 398 PHE 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 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 245 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 GLN Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.6980 chunk 133 optimal weight: 0.0270 chunk 3 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 270 ASN B 168 HIS ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN F 132 ASN F 318 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19647 Z= 0.247 Angle : 0.609 10.420 26742 Z= 0.315 Chirality : 0.045 0.172 2935 Planarity : 0.004 0.048 3462 Dihedral : 5.283 26.863 2674 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.16 % Favored : 92.76 % Rotamer: Outliers : 4.00 % Allowed : 14.95 % Favored : 81.06 % 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: -2.29 (0.16), residues: 2445 helix: -2.13 (0.64), residues: 48 sheet: -0.89 (0.17), residues: 905 loop : -1.98 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 330 HIS 0.008 0.001 HIS F 168 PHE 0.026 0.002 PHE C 356 TYR 0.040 0.001 TYR F 9 ARG 0.004 0.000 ARG E 73 *********************** 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 778 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 694 time to evaluate : 2.198 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: 0.7742 (t) cc_final: 0.7419 (t) REVERT: A 18 ILE cc_start: 0.8131 (pt) cc_final: 0.7903 (mm) REVERT: A 30 SER cc_start: 0.8143 (m) cc_final: 0.7649 (p) REVERT: A 35 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7606 (ttmm) REVERT: A 37 LYS cc_start: 0.8242 (mttt) cc_final: 0.7714 (mtmm) REVERT: A 42 VAL cc_start: 0.8511 (t) cc_final: 0.7993 (m) REVERT: A 45 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6834 (mm-30) REVERT: A 52 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8129 (ttpp) REVERT: A 75 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: A 76 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6330 (tm-30) REVERT: A 105 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7725 (mtpp) REVERT: A 108 VAL cc_start: 0.8843 (t) cc_final: 0.8358 (m) REVERT: A 111 SER cc_start: 0.8271 (t) cc_final: 0.7868 (t) REVERT: A 123 LYS cc_start: 0.7673 (mtmt) cc_final: 0.7306 (mtmt) REVERT: A 130 GLN cc_start: 0.7590 (tt0) cc_final: 0.7001 (tt0) REVERT: A 147 TYR cc_start: 0.7772 (m-10) cc_final: 0.7106 (m-80) REVERT: A 176 LYS cc_start: 0.8326 (mttt) cc_final: 0.7954 (mtpp) REVERT: A 205 SER cc_start: 0.8488 (t) cc_final: 0.8045 (p) REVERT: A 241 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 252 LYS cc_start: 0.8744 (tttt) cc_final: 0.8488 (ttmm) REVERT: A 269 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6607 (mt-10) REVERT: A 281 ASP cc_start: 0.7776 (t0) cc_final: 0.7413 (t0) REVERT: A 368 GLN cc_start: 0.7325 (tm-30) cc_final: 0.6908 (tm-30) REVERT: B 18 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7590 (ptm-80) REVERT: B 34 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 37 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7128 (mmtt) REVERT: B 62 LYS cc_start: 0.7340 (tttt) cc_final: 0.6825 (mtpp) REVERT: B 68 TYR cc_start: 0.8643 (p90) cc_final: 0.8337 (p90) REVERT: B 108 ASP cc_start: 0.7462 (p0) cc_final: 0.7059 (p0) REVERT: B 159 GLN cc_start: 0.7968 (mt0) cc_final: 0.7691 (mt0) REVERT: B 164 TYR cc_start: 0.8195 (m-80) cc_final: 0.7486 (m-80) REVERT: B 213 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7469 (mmtm) REVERT: B 230 ARG cc_start: 0.8425 (mtp85) cc_final: 0.8084 (ptp-110) REVERT: B 254 LYS cc_start: 0.7458 (mmmt) cc_final: 0.7254 (mmmt) REVERT: B 265 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7357 (mmmm) REVERT: B 324 LYS cc_start: 0.7714 (mtmm) cc_final: 0.7441 (mtmm) REVERT: B 336 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7828 (ttmm) REVERT: C 10 GLN cc_start: 0.7635 (tt0) cc_final: 0.7328 (tt0) REVERT: C 35 LYS cc_start: 0.8342 (tttt) cc_final: 0.7857 (tttm) REVERT: C 37 LYS cc_start: 0.7630 (ttmt) cc_final: 0.7129 (mtpt) REVERT: C 120 GLU cc_start: 0.7614 (pt0) cc_final: 0.7095 (pt0) REVERT: C 132 PHE cc_start: 0.7687 (m-10) cc_final: 0.7336 (m-10) REVERT: C 207 THR cc_start: 0.7941 (t) cc_final: 0.7640 (p) REVERT: C 214 TYR cc_start: 0.8305 (t80) cc_final: 0.7763 (t80) REVERT: C 222 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: C 242 GLN cc_start: 0.7710 (tp40) cc_final: 0.7490 (tp-100) REVERT: C 245 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7518 (mtpt) REVERT: C 252 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7962 (mtpp) REVERT: C 254 THR cc_start: 0.8457 (p) cc_final: 0.8177 (t) REVERT: C 260 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6713 (mt-10) REVERT: C 261 ILE cc_start: 0.8297 (mm) cc_final: 0.7921 (mm) REVERT: C 334 SER cc_start: 0.8532 (t) cc_final: 0.8025 (p) REVERT: C 338 THR cc_start: 0.7950 (m) cc_final: 0.7533 (t) REVERT: D 34 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 64 ARG cc_start: 0.7345 (mmm-85) cc_final: 0.6965 (mtt-85) REVERT: D 74 ILE cc_start: 0.8247 (mt) cc_final: 0.7935 (mt) REVERT: D 75 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8116 (mttm) REVERT: D 77 ILE cc_start: 0.8316 (mt) cc_final: 0.8081 (tt) REVERT: D 94 ASP cc_start: 0.6905 (t0) cc_final: 0.6682 (t0) REVERT: D 120 ARG cc_start: 0.6944 (tpt-90) cc_final: 0.6588 (tpt-90) REVERT: D 130 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7541 (mtmm) REVERT: D 180 SER cc_start: 0.8215 (p) cc_final: 0.7745 (m) REVERT: D 215 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7416 (ttmm) REVERT: D 241 ASP cc_start: 0.7811 (p0) cc_final: 0.7391 (p0) REVERT: D 242 LYS cc_start: 0.8188 (mttm) cc_final: 0.7805 (mttp) REVERT: D 254 LYS cc_start: 0.8595 (mtmp) cc_final: 0.8178 (mtpp) REVERT: D 261 LEU cc_start: 0.8672 (tp) cc_final: 0.7950 (mt) REVERT: D 265 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7791 (mmmm) REVERT: D 277 THR cc_start: 0.8259 (m) cc_final: 0.7798 (p) REVERT: D 338 PHE cc_start: 0.8075 (m-10) cc_final: 0.7836 (m-80) REVERT: D 354 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.2326 (tt0) REVERT: E 6 THR cc_start: 0.8178 (m) cc_final: 0.7793 (p) REVERT: E 15 TYR cc_start: 0.7285 (t80) cc_final: 0.7066 (t80) REVERT: E 35 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7709 (mtpp) REVERT: E 77 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7019 (mt0) REVERT: E 110 LYS cc_start: 0.8538 (ptpp) cc_final: 0.8223 (mtmm) REVERT: E 188 ASP cc_start: 0.7012 (t70) cc_final: 0.6591 (t70) REVERT: E 202 ASP cc_start: 0.8169 (p0) cc_final: 0.7952 (p0) REVERT: E 203 ILE cc_start: 0.8071 (mm) cc_final: 0.7746 (pt) REVERT: E 222 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7693 (mt0) REVERT: E 245 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7475 (mtpp) REVERT: E 246 ASP cc_start: 0.7133 (m-30) cc_final: 0.6778 (m-30) REVERT: E 253 PHE cc_start: 0.7809 (m-80) cc_final: 0.7604 (m-80) REVERT: E 257 PHE cc_start: 0.8038 (m-80) cc_final: 0.7773 (m-10) REVERT: E 269 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7178 (mt-10) REVERT: E 280 PHE cc_start: 0.8453 (m-10) cc_final: 0.8014 (m-10) REVERT: E 324 LYS cc_start: 0.8328 (mtmp) cc_final: 0.8117 (mtmm) REVERT: E 338 THR cc_start: 0.8504 (m) cc_final: 0.8186 (t) REVERT: E 340 LYS cc_start: 0.7742 (tttt) cc_final: 0.7405 (ttmt) REVERT: F 8 GLU cc_start: 0.7369 (tp30) cc_final: 0.7111 (tp30) REVERT: F 16 MET cc_start: 0.7996 (mtp) cc_final: 0.7745 (mtp) REVERT: F 57 SER cc_start: 0.8553 (p) cc_final: 0.7965 (t) REVERT: F 60 ASN cc_start: 0.7981 (m-40) cc_final: 0.7628 (m-40) REVERT: F 69 ASP cc_start: 0.7324 (t70) cc_final: 0.7059 (t70) REVERT: F 75 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7719 (mmtp) REVERT: F 76 GLU cc_start: 0.6596 (tp30) cc_final: 0.6241 (tp30) REVERT: F 129 VAL cc_start: 0.8149 (t) cc_final: 0.7761 (p) REVERT: F 175 ASP cc_start: 0.8410 (t0) cc_final: 0.7983 (t0) REVERT: F 177 SER cc_start: 0.8709 (m) cc_final: 0.8395 (p) REVERT: F 227 ARG cc_start: 0.7327 (tpp80) cc_final: 0.7071 (mmt-90) REVERT: F 241 ASP cc_start: 0.7579 (p0) cc_final: 0.7370 (p0) REVERT: F 245 LYS cc_start: 0.8151 (ptmt) cc_final: 0.7794 (ttpt) REVERT: F 261 LEU cc_start: 0.8547 (tp) cc_final: 0.8265 (mt) REVERT: F 286 LYS cc_start: 0.8305 (tppp) cc_final: 0.7910 (tppp) REVERT: F 290 LYS cc_start: 0.7793 (mttt) cc_final: 0.7497 (mttt) REVERT: H 38 ARG cc_start: 0.7196 (ptt-90) cc_final: 0.6796 (ptt-90) REVERT: H 76 ASN cc_start: 0.6477 (p0) cc_final: 0.5703 (p0) REVERT: L 20 THR cc_start: 0.8620 (t) cc_final: 0.8345 (p) REVERT: L 42 LYS cc_start: 0.8285 (mmmt) cc_final: 0.8005 (mmmt) REVERT: L 47 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8002 (mm) REVERT: L 104 VAL cc_start: 0.8064 (t) cc_final: 0.7833 (p) outliers start: 84 outliers final: 62 residues processed: 736 average time/residue: 0.3498 time to fit residues: 375.9728 Evaluate side-chains 736 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 669 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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 166 LEU 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 33 ILE 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 138 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 198 VAL 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 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 221 LEU Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 50 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 286 LYS Chi-restraints excluded: chain D residue 309 GLU 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 73 ARG Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 245 LYS 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 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 187 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 240 SER 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 47 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 235 GLN A 242 GLN A 270 ASN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 HIS E 20 ASN F 41 HIS F 52 GLN F 318 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 19647 Z= 0.411 Angle : 0.685 9.903 26742 Z= 0.357 Chirality : 0.047 0.182 2935 Planarity : 0.005 0.047 3462 Dihedral : 5.699 28.325 2674 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.85 % Favored : 92.07 % Rotamer: Outliers : 4.62 % Allowed : 15.52 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.27 (0.16), residues: 2445 helix: -2.30 (0.61), residues: 48 sheet: -0.78 (0.17), residues: 882 loop : -2.02 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 103 HIS 0.023 0.002 HIS B 168 PHE 0.024 0.002 PHE C 356 TYR 0.044 0.002 TYR F 9 ARG 0.006 0.001 ARG D 230 *********************** 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 785 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 688 time to evaluate : 2.088 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: 0.7753 (t) cc_final: 0.7442 (t) REVERT: A 18 ILE cc_start: 0.8235 (pt) cc_final: 0.7973 (mm) REVERT: A 30 SER cc_start: 0.8166 (m) cc_final: 0.7626 (p) REVERT: A 35 LYS cc_start: 0.8436 (ttmt) cc_final: 0.7622 (ttmm) REVERT: A 37 LYS cc_start: 0.8270 (mttt) cc_final: 0.7744 (mtmm) REVERT: A 42 VAL cc_start: 0.8630 (t) cc_final: 0.8152 (m) REVERT: A 45 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6912 (mm-30) REVERT: A 52 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8087 (ttpp) REVERT: A 75 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: A 76 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6397 (tm-30) REVERT: A 105 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7709 (mtpp) REVERT: A 111 SER cc_start: 0.8368 (t) cc_final: 0.7960 (t) REVERT: A 123 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7495 (mtmt) REVERT: A 130 GLN cc_start: 0.7610 (tt0) cc_final: 0.7350 (tt0) REVERT: A 136 THR cc_start: 0.7429 (m) cc_final: 0.7048 (p) REVERT: A 147 TYR cc_start: 0.7863 (m-10) cc_final: 0.7386 (m-10) REVERT: A 176 LYS cc_start: 0.8312 (mttt) cc_final: 0.7973 (mtpp) REVERT: A 183 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6299 (mt-10) REVERT: A 205 SER cc_start: 0.8523 (t) cc_final: 0.8003 (p) REVERT: A 241 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6812 (tm-30) REVERT: A 252 LYS cc_start: 0.8763 (tttt) cc_final: 0.8443 (ttmm) REVERT: A 269 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6749 (mt-10) REVERT: A 281 ASP cc_start: 0.7821 (t0) cc_final: 0.7481 (t0) REVERT: A 317 THR cc_start: 0.8096 (m) cc_final: 0.7845 (p) REVERT: A 368 GLN cc_start: 0.7387 (tm-30) cc_final: 0.6960 (tm-30) REVERT: B 18 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7657 (ptm-80) REVERT: B 34 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7089 (mm-30) REVERT: B 37 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7206 (mmtt) REVERT: B 68 TYR cc_start: 0.8660 (p90) cc_final: 0.8214 (p90) REVERT: B 108 ASP cc_start: 0.7516 (p0) cc_final: 0.7086 (p0) REVERT: B 164 TYR cc_start: 0.8349 (m-80) cc_final: 0.7558 (m-80) REVERT: B 213 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7453 (mmtm) REVERT: B 230 ARG cc_start: 0.8350 (mtp85) cc_final: 0.7978 (ptp-110) REVERT: B 254 LYS cc_start: 0.7512 (mmmt) cc_final: 0.7276 (mmmt) REVERT: B 265 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7417 (mmtt) REVERT: B 275 MET cc_start: 0.8050 (mpp) cc_final: 0.7602 (mmm) REVERT: B 290 LYS cc_start: 0.7384 (ttmt) cc_final: 0.7094 (ttmt) REVERT: B 302 ASP cc_start: 0.6851 (p0) cc_final: 0.6607 (p0) REVERT: B 324 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7532 (mtmm) REVERT: B 336 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7831 (ttmm) REVERT: C 10 GLN cc_start: 0.7654 (tt0) cc_final: 0.7316 (tt0) REVERT: C 35 LYS cc_start: 0.8368 (tttt) cc_final: 0.7830 (tttm) REVERT: C 76 GLU cc_start: 0.7755 (tp30) cc_final: 0.7035 (tp30) REVERT: C 132 PHE cc_start: 0.7648 (m-10) cc_final: 0.7341 (m-10) REVERT: C 186 ASN cc_start: 0.8289 (m-40) cc_final: 0.7968 (m-40) REVERT: C 207 THR cc_start: 0.7935 (t) cc_final: 0.7658 (p) REVERT: C 214 TYR cc_start: 0.8397 (t80) cc_final: 0.7649 (t80) REVERT: C 218 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8452 (m-40) REVERT: C 222 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: C 245 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7571 (mtpt) REVERT: C 254 THR cc_start: 0.8502 (p) cc_final: 0.8221 (t) REVERT: C 260 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6805 (mt-10) REVERT: C 261 ILE cc_start: 0.8373 (mm) cc_final: 0.8020 (mm) REVERT: C 288 THR cc_start: 0.6722 (OUTLIER) cc_final: 0.6371 (p) REVERT: C 334 SER cc_start: 0.8549 (t) cc_final: 0.8032 (p) REVERT: C 338 THR cc_start: 0.8051 (m) cc_final: 0.7650 (t) REVERT: C 394 HIS cc_start: 0.7541 (p90) cc_final: 0.7267 (p90) REVERT: D 34 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 64 ARG cc_start: 0.7395 (mmm-85) cc_final: 0.6976 (mtt-85) REVERT: D 74 ILE cc_start: 0.8193 (mt) cc_final: 0.7831 (mt) REVERT: D 75 LYS cc_start: 0.8572 (mmtt) cc_final: 0.7980 (mttm) REVERT: D 77 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8114 (tt) REVERT: D 120 ARG cc_start: 0.6961 (tpt-90) cc_final: 0.6600 (tpt-90) REVERT: D 130 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7518 (mtmm) REVERT: D 180 SER cc_start: 0.8094 (p) cc_final: 0.7500 (m) REVERT: D 215 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7496 (ttmm) REVERT: D 241 ASP cc_start: 0.7796 (p0) cc_final: 0.7359 (p0) REVERT: D 242 LYS cc_start: 0.8156 (mttm) cc_final: 0.7780 (mttp) REVERT: D 257 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8681 (m) REVERT: D 336 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7524 (tttt) REVERT: D 338 PHE cc_start: 0.8050 (m-10) cc_final: 0.7837 (m-80) REVERT: D 354 GLU cc_start: 0.5082 (OUTLIER) cc_final: 0.2714 (tp30) REVERT: E 6 THR cc_start: 0.8218 (m) cc_final: 0.7831 (p) REVERT: E 15 TYR cc_start: 0.7296 (t80) cc_final: 0.7089 (t80) REVERT: E 35 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7700 (mtpp) REVERT: E 99 GLU cc_start: 0.7299 (tt0) cc_final: 0.7043 (tt0) REVERT: E 110 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8241 (mtmm) REVERT: E 188 ASP cc_start: 0.7030 (t70) cc_final: 0.6610 (t70) REVERT: E 202 ASP cc_start: 0.8241 (p0) cc_final: 0.7931 (p0) REVERT: E 203 ILE cc_start: 0.8080 (mm) cc_final: 0.7581 (tt) REVERT: E 222 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7678 (mt0) REVERT: E 257 PHE cc_start: 0.8062 (m-80) cc_final: 0.7784 (m-10) REVERT: E 269 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7134 (mt-10) REVERT: E 280 PHE cc_start: 0.8460 (m-10) cc_final: 0.8027 (m-10) REVERT: E 304 ASN cc_start: 0.8065 (m110) cc_final: 0.7646 (m-40) REVERT: E 324 LYS cc_start: 0.8316 (mtmp) cc_final: 0.8088 (mtmm) REVERT: E 338 THR cc_start: 0.8547 (m) cc_final: 0.8234 (t) REVERT: E 340 LYS cc_start: 0.7818 (tttt) cc_final: 0.7460 (ttmt) REVERT: E 349 GLN cc_start: 0.7216 (tp40) cc_final: 0.6607 (tp40) REVERT: F 8 GLU cc_start: 0.7386 (tp30) cc_final: 0.7059 (tp30) REVERT: F 16 MET cc_start: 0.7978 (mtp) cc_final: 0.7748 (mtp) REVERT: F 57 SER cc_start: 0.8573 (p) cc_final: 0.8284 (t) REVERT: F 60 ASN cc_start: 0.8124 (m-40) cc_final: 0.7724 (m-40) REVERT: F 69 ASP cc_start: 0.7326 (t70) cc_final: 0.7107 (t0) REVERT: F 75 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8018 (mmtp) REVERT: F 129 VAL cc_start: 0.8181 (t) cc_final: 0.7818 (p) REVERT: F 175 ASP cc_start: 0.8454 (t0) cc_final: 0.8110 (t0) REVERT: F 177 SER cc_start: 0.8715 (m) cc_final: 0.8368 (p) REVERT: F 261 LEU cc_start: 0.8595 (tp) cc_final: 0.8362 (mt) REVERT: F 277 THR cc_start: 0.8196 (m) cc_final: 0.7947 (p) REVERT: F 290 LYS cc_start: 0.7867 (mttt) cc_final: 0.7558 (mttt) REVERT: H 38 ARG cc_start: 0.7272 (ptt-90) cc_final: 0.6911 (ptt-90) REVERT: H 76 ASN cc_start: 0.6697 (p0) cc_final: 0.5941 (p0) REVERT: H 83 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8057 (tmtt) REVERT: L 20 THR cc_start: 0.8616 (t) cc_final: 0.8300 (p) REVERT: L 42 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8056 (mmmt) REVERT: L 47 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8069 (mm) REVERT: L 90 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6292 (tm130) REVERT: L 104 VAL cc_start: 0.8152 (t) cc_final: 0.7892 (p) outliers start: 97 outliers final: 63 residues processed: 733 average time/residue: 0.3373 time to fit residues: 359.8550 Evaluate side-chains 756 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 683 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET 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 166 LEU 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 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 138 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 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 222 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 288 THR 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 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 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 20 ASN Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 94 CYS 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 369 ILE Chi-restraints excluded: chain E residue 377 LYS 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 187 THR Chi-restraints excluded: chain F residue 210 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 47 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 2.9990 chunk 26 optimal weight: 0.0270 chunk 133 optimal weight: 0.7980 chunk 171 optimal weight: 0.0770 chunk 197 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 234 optimal weight: 0.0050 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 196 GLN A 218 ASN A 270 ASN B 168 HIS C 66 GLN C 218 ASN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN E 20 ASN ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19647 Z= 0.161 Angle : 0.587 8.973 26742 Z= 0.303 Chirality : 0.044 0.166 2935 Planarity : 0.004 0.047 3462 Dihedral : 5.099 24.524 2674 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.76 % Allowed : 17.18 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.05 (0.17), residues: 2445 helix: -2.35 (0.62), residues: 49 sheet: -0.68 (0.17), residues: 890 loop : -1.82 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 330 HIS 0.005 0.001 HIS C 394 PHE 0.024 0.001 PHE C 356 TYR 0.025 0.001 TYR F 9 ARG 0.005 0.000 ARG E 21 *********************** 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 764 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 685 time to evaluate : 2.079 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: 0.7668 (t) cc_final: 0.7370 (t) REVERT: A 18 ILE cc_start: 0.7992 (pt) cc_final: 0.7761 (mm) REVERT: A 30 SER cc_start: 0.8035 (m) cc_final: 0.7588 (p) REVERT: A 35 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7732 (ttmm) REVERT: A 42 VAL cc_start: 0.8422 (t) cc_final: 0.7884 (m) REVERT: A 45 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6762 (mm-30) REVERT: A 52 LYS cc_start: 0.8312 (ttpt) cc_final: 0.8003 (ttpp) REVERT: A 76 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6444 (tm-30) REVERT: A 82 THR cc_start: 0.7558 (m) cc_final: 0.7171 (p) REVERT: A 105 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7684 (mtpp) REVERT: A 111 SER cc_start: 0.8371 (t) cc_final: 0.7962 (t) REVERT: A 123 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7383 (mtmt) REVERT: A 147 TYR cc_start: 0.7775 (m-10) cc_final: 0.7385 (m-80) REVERT: A 176 LYS cc_start: 0.8300 (mttt) cc_final: 0.7922 (mtpp) REVERT: A 205 SER cc_start: 0.8463 (t) cc_final: 0.8035 (p) REVERT: A 241 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6513 (tm-30) REVERT: A 245 LYS cc_start: 0.7733 (mtpt) cc_final: 0.7188 (mtpp) REVERT: A 252 LYS cc_start: 0.8742 (tttt) cc_final: 0.8418 (ttmm) REVERT: A 269 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6754 (mt-10) REVERT: A 281 ASP cc_start: 0.7735 (t0) cc_final: 0.7323 (t0) REVERT: A 368 GLN cc_start: 0.7342 (tm-30) cc_final: 0.6907 (tm-30) REVERT: B 18 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7680 (ptm-80) REVERT: B 34 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7166 (mm-30) REVERT: B 37 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7094 (mmtt) REVERT: B 62 LYS cc_start: 0.7435 (tttt) cc_final: 0.6933 (mtpp) REVERT: B 68 TYR cc_start: 0.8598 (p90) cc_final: 0.8247 (p90) REVERT: B 108 ASP cc_start: 0.7478 (p0) cc_final: 0.7054 (p0) REVERT: B 112 MET cc_start: 0.8350 (ttt) cc_final: 0.8124 (ttm) REVERT: B 164 TYR cc_start: 0.8262 (m-80) cc_final: 0.7427 (m-80) REVERT: B 175 ASP cc_start: 0.6807 (t0) cc_final: 0.6569 (m-30) REVERT: B 236 TRP cc_start: 0.8703 (m-10) cc_final: 0.8217 (m-10) REVERT: B 254 LYS cc_start: 0.7511 (mmmt) cc_final: 0.7282 (mmmt) REVERT: B 275 MET cc_start: 0.8024 (mpp) cc_final: 0.7594 (mmm) REVERT: B 283 VAL cc_start: 0.8205 (t) cc_final: 0.7924 (m) REVERT: B 324 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7384 (mtmm) REVERT: B 336 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7815 (ttmm) REVERT: C 10 GLN cc_start: 0.7626 (tt0) cc_final: 0.7318 (tt0) REVERT: C 120 GLU cc_start: 0.7514 (pt0) cc_final: 0.7022 (pt0) REVERT: C 132 PHE cc_start: 0.7613 (m-10) cc_final: 0.7323 (m-10) REVERT: C 178 VAL cc_start: 0.7916 (t) cc_final: 0.7424 (p) REVERT: C 186 ASN cc_start: 0.8213 (m-40) cc_final: 0.8006 (m-40) REVERT: C 207 THR cc_start: 0.7909 (t) cc_final: 0.7647 (p) REVERT: C 214 TYR cc_start: 0.8458 (t80) cc_final: 0.7525 (t80) REVERT: C 218 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8418 (m-40) REVERT: C 222 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: C 245 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7586 (mtpt) REVERT: C 260 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6674 (mt-10) REVERT: C 261 ILE cc_start: 0.8288 (mm) cc_final: 0.7811 (mm) REVERT: C 288 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6200 (p) REVERT: C 338 THR cc_start: 0.8040 (m) cc_final: 0.7655 (t) REVERT: C 394 HIS cc_start: 0.7505 (p90) cc_final: 0.7257 (p90) REVERT: D 34 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7184 (mm-30) REVERT: D 64 ARG cc_start: 0.7303 (mmm-85) cc_final: 0.6941 (mtp85) REVERT: D 74 ILE cc_start: 0.8150 (mt) cc_final: 0.7869 (mt) REVERT: D 77 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8107 (tt) REVERT: D 130 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7501 (mtmm) REVERT: D 180 SER cc_start: 0.8234 (p) cc_final: 0.7599 (m) REVERT: D 215 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7408 (ttmm) REVERT: D 227 ARG cc_start: 0.7615 (ttm110) cc_final: 0.6725 (tpp80) REVERT: D 241 ASP cc_start: 0.7803 (p0) cc_final: 0.7452 (p0) REVERT: D 242 LYS cc_start: 0.8141 (mttm) cc_final: 0.7800 (mttp) REVERT: D 257 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8662 (m) REVERT: D 338 PHE cc_start: 0.8025 (m-10) cc_final: 0.7815 (m-80) REVERT: E 6 THR cc_start: 0.8152 (m) cc_final: 0.7774 (p) REVERT: E 15 TYR cc_start: 0.7244 (t80) cc_final: 0.7030 (t80) REVERT: E 35 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7708 (mtpp) REVERT: E 55 MET cc_start: 0.7274 (mtm) cc_final: 0.7070 (mtm) REVERT: E 110 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8147 (mtmm) REVERT: E 188 ASP cc_start: 0.7014 (t70) cc_final: 0.6608 (t70) REVERT: E 202 ASP cc_start: 0.8204 (p0) cc_final: 0.7978 (p0) REVERT: E 203 ILE cc_start: 0.8060 (mm) cc_final: 0.7754 (pt) REVERT: E 222 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7700 (mt0) REVERT: E 246 ASP cc_start: 0.7048 (m-30) cc_final: 0.6663 (m-30) REVERT: E 262 TYR cc_start: 0.7413 (m-80) cc_final: 0.6296 (m-80) REVERT: E 269 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7274 (mt-10) REVERT: E 280 PHE cc_start: 0.8396 (m-10) cc_final: 0.7913 (m-10) REVERT: E 282 ILE cc_start: 0.8425 (mm) cc_final: 0.8208 (mm) REVERT: E 304 ASN cc_start: 0.8002 (m110) cc_final: 0.7596 (m-40) REVERT: E 324 LYS cc_start: 0.8314 (mtmp) cc_final: 0.8097 (mtmm) REVERT: E 338 THR cc_start: 0.8524 (m) cc_final: 0.8201 (t) REVERT: E 340 LYS cc_start: 0.7729 (tttt) cc_final: 0.7404 (ttmt) REVERT: F 8 GLU cc_start: 0.7339 (tp30) cc_final: 0.7051 (tp30) REVERT: F 16 MET cc_start: 0.7948 (mtp) cc_final: 0.7735 (mtp) REVERT: F 34 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6805 (mt-10) REVERT: F 37 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7266 (mmtm) REVERT: F 57 SER cc_start: 0.8587 (p) cc_final: 0.8296 (t) REVERT: F 60 ASN cc_start: 0.7963 (m-40) cc_final: 0.7645 (m-40) REVERT: F 75 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7971 (mmtp) REVERT: F 115 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7461 (mttm) REVERT: F 175 ASP cc_start: 0.8396 (t0) cc_final: 0.7979 (t0) REVERT: F 177 SER cc_start: 0.8707 (m) cc_final: 0.8394 (p) REVERT: F 222 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7919 (mtpt) REVERT: F 227 ARG cc_start: 0.7192 (tpp80) cc_final: 0.6940 (mmt-90) REVERT: F 261 LEU cc_start: 0.8491 (tp) cc_final: 0.8258 (mt) REVERT: F 277 THR cc_start: 0.8205 (m) cc_final: 0.7948 (p) REVERT: F 290 LYS cc_start: 0.7722 (mttt) cc_final: 0.7483 (mttt) REVERT: H 38 ARG cc_start: 0.7224 (ptt-90) cc_final: 0.6828 (ptt-90) REVERT: H 40 SER cc_start: 0.8310 (p) cc_final: 0.7617 (t) REVERT: H 76 ASN cc_start: 0.6500 (p0) cc_final: 0.5709 (p0) REVERT: H 83 LYS cc_start: 0.8371 (tmtt) cc_final: 0.8003 (tptp) REVERT: L 20 THR cc_start: 0.8608 (t) cc_final: 0.8325 (p) REVERT: L 42 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7968 (mmmt) REVERT: L 90 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6349 (tm130) REVERT: L 104 VAL cc_start: 0.8085 (t) cc_final: 0.7843 (p) outliers start: 79 outliers final: 45 residues processed: 721 average time/residue: 0.3513 time to fit residues: 366.6969 Evaluate side-chains 728 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 676 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 81 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 77 ILE 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 257 VAL 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 318 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain F residue 34 GLU 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 H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 0.0870 chunk 213 optimal weight: 0.0270 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 196 GLN A 218 ASN A 270 ASN B 168 HIS C 157 ASN C 218 ASN ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19647 Z= 0.182 Angle : 0.593 8.373 26742 Z= 0.306 Chirality : 0.044 0.168 2935 Planarity : 0.004 0.045 3462 Dihedral : 5.004 24.716 2674 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.81 % Allowed : 18.04 % Favored : 78.15 % 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: -1.84 (0.17), residues: 2445 helix: -2.24 (0.62), residues: 49 sheet: -0.51 (0.17), residues: 880 loop : -1.69 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.008 0.001 HIS B 168 PHE 0.016 0.001 PHE C 156 TYR 0.033 0.001 TYR F 9 ARG 0.003 0.000 ARG B 298 *********************** 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 768 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 688 time to evaluate : 2.336 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: 0.7700 (t) cc_final: 0.7381 (t) REVERT: A 18 ILE cc_start: 0.8001 (pt) cc_final: 0.7785 (mm) REVERT: A 30 SER cc_start: 0.8053 (m) cc_final: 0.7620 (p) REVERT: A 35 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7655 (ttmm) REVERT: A 37 LYS cc_start: 0.8351 (mtmm) cc_final: 0.7881 (mtmm) REVERT: A 42 VAL cc_start: 0.8396 (t) cc_final: 0.7858 (m) REVERT: A 45 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6796 (mm-30) REVERT: A 52 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7989 (ttpp) REVERT: A 76 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6431 (tm-30) REVERT: A 105 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7692 (mtpp) REVERT: A 111 SER cc_start: 0.8388 (t) cc_final: 0.8026 (t) REVERT: A 123 LYS cc_start: 0.7623 (mtmt) cc_final: 0.7259 (mtmt) REVERT: A 147 TYR cc_start: 0.7799 (m-10) cc_final: 0.7467 (m-80) REVERT: A 168 THR cc_start: 0.8585 (m) cc_final: 0.8375 (t) REVERT: A 176 LYS cc_start: 0.8300 (mttt) cc_final: 0.7924 (mtpp) REVERT: A 205 SER cc_start: 0.8474 (t) cc_final: 0.8030 (p) REVERT: A 241 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6592 (tm-30) REVERT: A 245 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7311 (mtpp) REVERT: A 252 LYS cc_start: 0.8741 (tttt) cc_final: 0.8421 (ttmm) REVERT: A 269 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6794 (mt-10) REVERT: A 281 ASP cc_start: 0.7743 (t0) cc_final: 0.7364 (t0) REVERT: A 368 GLN cc_start: 0.7341 (tm-30) cc_final: 0.6899 (tm-30) REVERT: B 18 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7619 (ttt-90) REVERT: B 34 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 37 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7121 (mmtt) REVERT: B 68 TYR cc_start: 0.8615 (p90) cc_final: 0.8244 (p90) REVERT: B 108 ASP cc_start: 0.7394 (p0) cc_final: 0.7056 (p0) REVERT: B 112 MET cc_start: 0.8406 (ttt) cc_final: 0.8188 (ttm) REVERT: B 164 TYR cc_start: 0.8260 (m-80) cc_final: 0.7419 (m-80) REVERT: B 175 ASP cc_start: 0.6729 (t0) cc_final: 0.6383 (m-30) REVERT: B 213 LYS cc_start: 0.8020 (mptt) cc_final: 0.7588 (mmmm) REVERT: B 236 TRP cc_start: 0.8720 (m-10) cc_final: 0.8293 (m-10) REVERT: B 254 LYS cc_start: 0.7501 (mmmt) cc_final: 0.7268 (mmmt) REVERT: B 265 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7529 (mmtt) REVERT: B 275 MET cc_start: 0.8073 (mpp) cc_final: 0.7607 (mmm) REVERT: B 324 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7389 (mtmm) REVERT: B 336 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7875 (ttmm) REVERT: C 10 GLN cc_start: 0.7620 (tt0) cc_final: 0.7306 (tt0) REVERT: C 76 GLU cc_start: 0.7820 (tp30) cc_final: 0.7592 (tp30) REVERT: C 105 LYS cc_start: 0.7500 (tttp) cc_final: 0.7220 (tttp) REVERT: C 114 CYS cc_start: 0.5661 (t) cc_final: 0.5345 (t) REVERT: C 120 GLU cc_start: 0.7537 (pt0) cc_final: 0.7005 (pt0) REVERT: C 132 PHE cc_start: 0.7607 (m-10) cc_final: 0.7329 (m-10) REVERT: C 178 VAL cc_start: 0.7940 (t) cc_final: 0.7436 (p) REVERT: C 186 ASN cc_start: 0.8228 (m-40) cc_final: 0.8011 (m-40) REVERT: C 207 THR cc_start: 0.7913 (t) cc_final: 0.7646 (p) REVERT: C 222 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7438 (mt0) REVERT: C 245 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7580 (mtpt) REVERT: C 260 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6746 (mt-10) REVERT: C 261 ILE cc_start: 0.8353 (mm) cc_final: 0.7934 (mm) REVERT: C 288 THR cc_start: 0.6486 (OUTLIER) cc_final: 0.6121 (p) REVERT: C 338 THR cc_start: 0.8043 (m) cc_final: 0.7668 (t) REVERT: C 394 HIS cc_start: 0.7500 (p90) cc_final: 0.7223 (p90) REVERT: D 34 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7120 (mm-30) REVERT: D 64 ARG cc_start: 0.7316 (mmm-85) cc_final: 0.6956 (mtp85) REVERT: D 74 ILE cc_start: 0.8141 (mt) cc_final: 0.7834 (mt) REVERT: D 88 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7414 (ptt90) REVERT: D 130 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7490 (mtmm) REVERT: D 180 SER cc_start: 0.8259 (p) cc_final: 0.7633 (m) REVERT: D 215 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7433 (ttmm) REVERT: D 227 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7139 (tpp80) REVERT: D 241 ASP cc_start: 0.7788 (p0) cc_final: 0.7577 (p0) REVERT: D 242 LYS cc_start: 0.8172 (mttm) cc_final: 0.7789 (mttm) REVERT: D 257 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8658 (m) REVERT: D 354 GLU cc_start: 0.4971 (OUTLIER) cc_final: 0.2661 (tp30) REVERT: E 6 THR cc_start: 0.8165 (m) cc_final: 0.7823 (p) REVERT: E 15 TYR cc_start: 0.7257 (t80) cc_final: 0.7014 (t80) REVERT: E 35 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7734 (mtpp) REVERT: E 66 GLN cc_start: 0.7064 (mt0) cc_final: 0.6856 (pt0) REVERT: E 77 GLN cc_start: 0.7436 (mm-40) cc_final: 0.6995 (mt0) REVERT: E 99 GLU cc_start: 0.7149 (tt0) cc_final: 0.6857 (tt0) REVERT: E 110 LYS cc_start: 0.8491 (ptpp) cc_final: 0.8216 (mtmm) REVERT: E 176 LYS cc_start: 0.7992 (mttp) cc_final: 0.7775 (mttp) REVERT: E 188 ASP cc_start: 0.7028 (t70) cc_final: 0.6564 (t70) REVERT: E 202 ASP cc_start: 0.8196 (p0) cc_final: 0.7981 (p0) REVERT: E 203 ILE cc_start: 0.8039 (mm) cc_final: 0.7731 (pt) REVERT: E 222 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7708 (mt0) REVERT: E 257 PHE cc_start: 0.8068 (m-80) cc_final: 0.7826 (m-10) REVERT: E 262 TYR cc_start: 0.7434 (m-80) cc_final: 0.6417 (m-80) REVERT: E 269 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7294 (mt-10) REVERT: E 280 PHE cc_start: 0.8416 (m-10) cc_final: 0.7950 (m-10) REVERT: E 304 ASN cc_start: 0.8026 (m110) cc_final: 0.7613 (m-40) REVERT: E 324 LYS cc_start: 0.8337 (mtmp) cc_final: 0.7649 (mtmm) REVERT: E 338 THR cc_start: 0.8532 (m) cc_final: 0.8194 (t) REVERT: E 340 LYS cc_start: 0.7756 (tttt) cc_final: 0.7418 (ttmt) REVERT: F 8 GLU cc_start: 0.7324 (tp30) cc_final: 0.7044 (tp30) REVERT: F 16 MET cc_start: 0.7957 (mtp) cc_final: 0.7740 (mtp) REVERT: F 37 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7284 (mmtm) REVERT: F 57 SER cc_start: 0.8586 (p) cc_final: 0.8302 (t) REVERT: F 60 ASN cc_start: 0.7958 (m-40) cc_final: 0.7638 (m-40) REVERT: F 75 LYS cc_start: 0.8286 (mmtt) cc_final: 0.8023 (mmtp) REVERT: F 115 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7429 (mttm) REVERT: F 175 ASP cc_start: 0.8393 (t0) cc_final: 0.7989 (t0) REVERT: F 177 SER cc_start: 0.8732 (m) cc_final: 0.8403 (p) REVERT: F 206 LYS cc_start: 0.6154 (tptt) cc_final: 0.5881 (tptt) REVERT: F 227 ARG cc_start: 0.7196 (tpp80) cc_final: 0.6926 (mmt-90) REVERT: F 261 LEU cc_start: 0.8516 (tp) cc_final: 0.8301 (mt) REVERT: F 286 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7869 (tppp) REVERT: F 290 LYS cc_start: 0.7752 (mttt) cc_final: 0.7477 (mttt) REVERT: H 38 ARG cc_start: 0.7237 (ptt-90) cc_final: 0.6845 (ptt-90) REVERT: H 76 ASN cc_start: 0.6471 (p0) cc_final: 0.5675 (p0) REVERT: H 83 LYS cc_start: 0.8356 (tmtt) cc_final: 0.7998 (tptp) REVERT: L 20 THR cc_start: 0.8601 (t) cc_final: 0.8318 (p) REVERT: L 42 LYS cc_start: 0.8293 (mmmt) cc_final: 0.8027 (mmmt) REVERT: L 90 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6355 (tm130) REVERT: L 104 VAL cc_start: 0.8115 (t) cc_final: 0.7883 (p) outliers start: 80 outliers final: 58 residues processed: 724 average time/residue: 0.3547 time to fit residues: 377.0829 Evaluate side-chains 739 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 674 time to evaluate : 2.091 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 260 GLU 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 81 GLN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 66 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 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 242 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 286 LYS 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 69 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 318 VAL 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 11 LEU Chi-restraints excluded: chain F residue 34 GLU 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 F residue 286 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 197 optimal weight: 6.9990 chunk 206 optimal weight: 0.0980 chunk 217 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 E 204 GLN ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19647 Z= 0.196 Angle : 0.601 9.469 26742 Z= 0.309 Chirality : 0.045 0.170 2935 Planarity : 0.004 0.044 3462 Dihedral : 4.975 24.097 2674 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.43 % Allowed : 18.94 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.76 (0.17), residues: 2445 helix: -2.07 (0.64), residues: 49 sheet: -0.44 (0.17), residues: 875 loop : -1.64 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.008 0.001 HIS B 168 PHE 0.018 0.001 PHE D 338 TYR 0.035 0.001 TYR B 238 ARG 0.003 0.000 ARG D 21 *********************** 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 745 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 673 time to evaluate : 1.985 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: 0.7706 (t) cc_final: 0.7394 (t) REVERT: A 18 ILE cc_start: 0.8007 (pt) cc_final: 0.7779 (mm) REVERT: A 30 SER cc_start: 0.8057 (m) cc_final: 0.7644 (p) REVERT: A 35 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7661 (ttmm) REVERT: A 37 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7808 (mtmm) REVERT: A 42 VAL cc_start: 0.8380 (t) cc_final: 0.7847 (m) REVERT: A 45 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 52 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8039 (ttpp) REVERT: A 76 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 105 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7670 (mtpp) REVERT: A 111 SER cc_start: 0.8436 (t) cc_final: 0.8067 (t) REVERT: A 123 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7236 (mtmt) REVERT: A 147 TYR cc_start: 0.7816 (m-10) cc_final: 0.7503 (m-80) REVERT: A 176 LYS cc_start: 0.8248 (mttt) cc_final: 0.7864 (mtpp) REVERT: A 205 SER cc_start: 0.8476 (t) cc_final: 0.8031 (p) REVERT: A 241 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6601 (tm-30) REVERT: A 245 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7303 (mtpp) REVERT: A 252 LYS cc_start: 0.8747 (tttt) cc_final: 0.8416 (ttmm) REVERT: A 269 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6802 (mt-10) REVERT: A 281 ASP cc_start: 0.7749 (t0) cc_final: 0.7360 (t0) REVERT: A 341 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 368 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6857 (tm-30) REVERT: B 18 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7654 (ttt-90) REVERT: B 34 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7184 (mm-30) REVERT: B 37 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7130 (mmtt) REVERT: B 62 LYS cc_start: 0.7489 (tttt) cc_final: 0.6957 (mtpp) REVERT: B 68 TYR cc_start: 0.8626 (p90) cc_final: 0.8255 (p90) REVERT: B 108 ASP cc_start: 0.7387 (p0) cc_final: 0.7053 (p0) REVERT: B 112 MET cc_start: 0.8394 (ttt) cc_final: 0.8162 (ttm) REVERT: B 164 TYR cc_start: 0.8282 (m-80) cc_final: 0.7433 (m-80) REVERT: B 175 ASP cc_start: 0.6808 (t0) cc_final: 0.6527 (m-30) REVERT: B 213 LYS cc_start: 0.8004 (mptt) cc_final: 0.7524 (mmmm) REVERT: B 236 TRP cc_start: 0.8668 (m-10) cc_final: 0.8192 (m-10) REVERT: B 254 LYS cc_start: 0.7485 (mmmt) cc_final: 0.7245 (mmmt) REVERT: B 265 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7543 (mmtt) REVERT: B 275 MET cc_start: 0.8054 (mpp) cc_final: 0.7615 (mmm) REVERT: B 324 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7401 (mtmm) REVERT: B 336 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7824 (ttmm) REVERT: C 10 GLN cc_start: 0.7610 (tt0) cc_final: 0.7290 (tt0) REVERT: C 105 LYS cc_start: 0.7482 (tttp) cc_final: 0.7272 (tttp) REVERT: C 107 TYR cc_start: 0.7597 (p90) cc_final: 0.6954 (p90) REVERT: C 114 CYS cc_start: 0.5553 (t) cc_final: 0.5301 (t) REVERT: C 120 GLU cc_start: 0.7562 (pt0) cc_final: 0.7023 (pt0) REVERT: C 132 PHE cc_start: 0.7584 (m-10) cc_final: 0.7312 (m-10) REVERT: C 207 THR cc_start: 0.7898 (t) cc_final: 0.7614 (p) REVERT: C 222 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7501 (mt0) REVERT: C 245 LYS cc_start: 0.7800 (mtpt) cc_final: 0.7584 (mtpt) REVERT: C 288 THR cc_start: 0.6499 (OUTLIER) cc_final: 0.6145 (p) REVERT: C 338 THR cc_start: 0.8044 (m) cc_final: 0.7671 (t) REVERT: C 394 HIS cc_start: 0.7486 (p90) cc_final: 0.7272 (p90) REVERT: D 34 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7150 (mm-30) REVERT: D 64 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.6963 (mtp85) REVERT: D 74 ILE cc_start: 0.8133 (mt) cc_final: 0.7819 (mt) REVERT: D 88 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7421 (ptt90) REVERT: D 130 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7574 (mtmm) REVERT: D 147 VAL cc_start: 0.8444 (p) cc_final: 0.8073 (m) REVERT: D 180 SER cc_start: 0.8271 (p) cc_final: 0.7702 (m) REVERT: D 215 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7438 (ttmm) REVERT: D 227 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7172 (tpp80) REVERT: D 257 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8661 (m) REVERT: D 337 ARG cc_start: 0.8473 (ttm170) cc_final: 0.8005 (mtt180) REVERT: D 354 GLU cc_start: 0.5007 (OUTLIER) cc_final: 0.2597 (tp30) REVERT: E 6 THR cc_start: 0.8185 (m) cc_final: 0.7859 (p) REVERT: E 15 TYR cc_start: 0.7245 (t80) cc_final: 0.7028 (t80) REVERT: E 35 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7751 (mtpp) REVERT: E 77 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7016 (mt0) REVERT: E 110 LYS cc_start: 0.8473 (ptpp) cc_final: 0.8186 (mtmm) REVERT: E 176 LYS cc_start: 0.8012 (mttp) cc_final: 0.7810 (mttp) REVERT: E 188 ASP cc_start: 0.7060 (t70) cc_final: 0.6610 (t70) REVERT: E 202 ASP cc_start: 0.8207 (p0) cc_final: 0.7967 (p0) REVERT: E 203 ILE cc_start: 0.8051 (mm) cc_final: 0.7729 (pt) REVERT: E 222 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7703 (mt0) REVERT: E 246 ASP cc_start: 0.7090 (m-30) cc_final: 0.6769 (m-30) REVERT: E 257 PHE cc_start: 0.8083 (m-80) cc_final: 0.7808 (m-10) REVERT: E 269 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7280 (mt-10) REVERT: E 280 PHE cc_start: 0.8431 (m-10) cc_final: 0.7944 (m-10) REVERT: E 304 ASN cc_start: 0.8019 (m110) cc_final: 0.7614 (m-40) REVERT: E 324 LYS cc_start: 0.8349 (mtmp) cc_final: 0.7683 (mtmm) REVERT: E 338 THR cc_start: 0.8541 (m) cc_final: 0.8198 (t) REVERT: E 340 LYS cc_start: 0.7740 (tttt) cc_final: 0.7419 (ttmt) REVERT: F 8 GLU cc_start: 0.7352 (tp30) cc_final: 0.7051 (tp30) REVERT: F 37 LYS cc_start: 0.7630 (mmtt) cc_final: 0.7319 (mmtm) REVERT: F 57 SER cc_start: 0.8596 (p) cc_final: 0.8317 (t) REVERT: F 60 ASN cc_start: 0.7952 (m-40) cc_final: 0.7641 (m-40) REVERT: F 70 MET cc_start: 0.7524 (tpp) cc_final: 0.7260 (mmm) REVERT: F 75 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8082 (mmtp) REVERT: F 129 VAL cc_start: 0.8129 (t) cc_final: 0.7705 (p) REVERT: F 175 ASP cc_start: 0.8395 (t0) cc_final: 0.8000 (t0) REVERT: F 177 SER cc_start: 0.8736 (m) cc_final: 0.8397 (p) REVERT: F 206 LYS cc_start: 0.6295 (tptt) cc_final: 0.6006 (tptt) REVERT: F 261 LEU cc_start: 0.8520 (tp) cc_final: 0.8298 (mt) REVERT: F 277 THR cc_start: 0.8190 (m) cc_final: 0.7918 (p) REVERT: F 286 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7897 (tppp) REVERT: F 290 LYS cc_start: 0.7752 (mttt) cc_final: 0.7497 (mttt) REVERT: H 38 ARG cc_start: 0.7248 (ptt-90) cc_final: 0.6882 (ptt-90) REVERT: H 83 LYS cc_start: 0.8355 (tmtt) cc_final: 0.7998 (tptp) REVERT: L 20 THR cc_start: 0.8607 (t) cc_final: 0.8312 (p) REVERT: L 42 LYS cc_start: 0.8287 (mmmt) cc_final: 0.8020 (mmmt) REVERT: L 90 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6345 (tm130) REVERT: L 104 VAL cc_start: 0.8137 (t) cc_final: 0.7909 (p) outliers start: 72 outliers final: 58 residues processed: 707 average time/residue: 0.3462 time to fit residues: 355.3333 Evaluate side-chains 737 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 672 time to evaluate : 2.091 ------------------------------------------------------------------------------- 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 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 A residue 340 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 81 GLN Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 222 LYS 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 66 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 VAL 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 94 CYS Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 286 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 4.9990 chunk 140 optimal weight: 0.1980 chunk 109 optimal weight: 0.2980 chunk 160 optimal weight: 4.9990 chunk 242 optimal weight: 0.8980 chunk 222 optimal weight: 0.4980 chunk 192 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 153 optimal weight: 0.0270 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 C 218 ASN C 270 ASN E 204 GLN E 368 GLN ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19647 Z= 0.167 Angle : 0.596 8.993 26742 Z= 0.307 Chirality : 0.044 0.166 2935 Planarity : 0.004 0.042 3462 Dihedral : 4.891 23.082 2674 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.05 % Allowed : 19.80 % Favored : 77.15 % 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: -1.67 (0.17), residues: 2445 helix: -1.83 (0.67), residues: 49 sheet: -0.36 (0.17), residues: 871 loop : -1.60 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.006 0.001 HIS B 168 PHE 0.018 0.001 PHE C 356 TYR 0.026 0.001 TYR F 9 ARG 0.003 0.000 ARG L 24 ********************** 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 747 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 683 time to evaluate : 2.284 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: 0.7660 (t) cc_final: 0.7352 (t) REVERT: A 30 SER cc_start: 0.8005 (m) cc_final: 0.7582 (p) REVERT: A 35 LYS cc_start: 0.8455 (ttmt) cc_final: 0.7571 (ttmm) REVERT: A 42 VAL cc_start: 0.8222 (t) cc_final: 0.7741 (m) REVERT: A 45 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6804 (mm-30) REVERT: A 52 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7868 (ttpp) REVERT: A 76 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6416 (tm-30) REVERT: A 105 LYS cc_start: 0.8102 (ttmt) cc_final: 0.7670 (mtpp) REVERT: A 110 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8351 (mtmm) REVERT: A 111 SER cc_start: 0.8403 (t) cc_final: 0.7993 (t) REVERT: A 123 LYS cc_start: 0.7547 (mtmt) cc_final: 0.7328 (mtmt) REVERT: A 176 LYS cc_start: 0.8246 (mttt) cc_final: 0.7862 (mtpp) REVERT: A 205 SER cc_start: 0.8469 (t) cc_final: 0.8046 (p) REVERT: A 241 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6579 (tm-30) REVERT: A 245 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7181 (mtpp) REVERT: A 252 LYS cc_start: 0.8733 (tttt) cc_final: 0.8412 (ttmm) REVERT: A 269 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6775 (mt-10) REVERT: A 324 LYS cc_start: 0.8466 (tttt) cc_final: 0.8171 (ttmm) REVERT: A 341 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7147 (mm-30) REVERT: A 368 GLN cc_start: 0.7300 (tm-30) cc_final: 0.6874 (tm-30) REVERT: B 18 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7678 (ttt-90) REVERT: B 34 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7209 (mm-30) REVERT: B 37 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7073 (mmtt) REVERT: B 44 TYR cc_start: 0.8086 (m-80) cc_final: 0.7337 (m-80) REVERT: B 68 TYR cc_start: 0.8593 (p90) cc_final: 0.8234 (p90) REVERT: B 108 ASP cc_start: 0.7388 (p0) cc_final: 0.7051 (p0) REVERT: B 112 MET cc_start: 0.8372 (ttt) cc_final: 0.8146 (ttm) REVERT: B 164 TYR cc_start: 0.8288 (m-80) cc_final: 0.7538 (m-80) REVERT: B 166 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6585 (mt-10) REVERT: B 175 ASP cc_start: 0.6805 (t0) cc_final: 0.6434 (m-30) REVERT: B 213 LYS cc_start: 0.7952 (mptt) cc_final: 0.7494 (mmmm) REVERT: B 230 ARG cc_start: 0.8528 (ptp-110) cc_final: 0.8320 (ptp-110) REVERT: B 236 TRP cc_start: 0.8667 (m-10) cc_final: 0.8216 (m-10) REVERT: B 275 MET cc_start: 0.8075 (mpp) cc_final: 0.7603 (mmm) REVERT: B 324 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7394 (mtmm) REVERT: B 336 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7818 (ttmm) REVERT: C 10 GLN cc_start: 0.7571 (tt0) cc_final: 0.7242 (tt0) REVERT: C 105 LYS cc_start: 0.7423 (tttp) cc_final: 0.7123 (tttp) REVERT: C 107 TYR cc_start: 0.7559 (p90) cc_final: 0.6906 (p90) REVERT: C 114 CYS cc_start: 0.5508 (t) cc_final: 0.5259 (t) REVERT: C 120 GLU cc_start: 0.7502 (pt0) cc_final: 0.6980 (pt0) REVERT: C 125 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7803 (p90) REVERT: C 132 PHE cc_start: 0.7584 (m-10) cc_final: 0.7262 (m-10) REVERT: C 207 THR cc_start: 0.7888 (t) cc_final: 0.7615 (p) REVERT: C 214 TYR cc_start: 0.8490 (t80) cc_final: 0.7621 (t80) REVERT: C 222 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: C 288 THR cc_start: 0.6388 (OUTLIER) cc_final: 0.5753 (p) REVERT: C 338 THR cc_start: 0.8058 (m) cc_final: 0.7694 (t) REVERT: C 394 HIS cc_start: 0.7483 (p90) cc_final: 0.7267 (p90) REVERT: D 64 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6918 (mtp85) REVERT: D 74 ILE cc_start: 0.8148 (mt) cc_final: 0.7841 (mt) REVERT: D 130 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7595 (mtmm) REVERT: D 147 VAL cc_start: 0.8251 (p) cc_final: 0.8051 (m) REVERT: D 215 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7431 (ttmm) REVERT: D 227 ARG cc_start: 0.7537 (ttm110) cc_final: 0.7201 (tpp80) REVERT: D 257 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8656 (m) REVERT: D 336 LYS cc_start: 0.7795 (mttt) cc_final: 0.7565 (tttt) REVERT: D 337 ARG cc_start: 0.8479 (ttm170) cc_final: 0.7991 (mtt180) REVERT: D 354 GLU cc_start: 0.4972 (OUTLIER) cc_final: 0.1707 (tp30) REVERT: E 6 THR cc_start: 0.8152 (m) cc_final: 0.7837 (p) REVERT: E 15 TYR cc_start: 0.7243 (t80) cc_final: 0.7041 (t80) REVERT: E 27 LEU cc_start: 0.8405 (tp) cc_final: 0.8071 (tt) REVERT: E 35 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7799 (mtpp) REVERT: E 77 GLN cc_start: 0.7449 (mm-40) cc_final: 0.6992 (mt0) REVERT: E 110 LYS cc_start: 0.8443 (ptpp) cc_final: 0.8159 (mtmm) REVERT: E 188 ASP cc_start: 0.7067 (t70) cc_final: 0.6661 (t70) REVERT: E 202 ASP cc_start: 0.8182 (p0) cc_final: 0.7952 (p0) REVERT: E 203 ILE cc_start: 0.8024 (mm) cc_final: 0.7726 (pt) REVERT: E 222 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7711 (mt0) REVERT: E 246 ASP cc_start: 0.7018 (m-30) cc_final: 0.6656 (m-30) REVERT: E 257 PHE cc_start: 0.8064 (m-80) cc_final: 0.7813 (m-10) REVERT: E 269 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7359 (mt-10) REVERT: E 280 PHE cc_start: 0.8410 (m-10) cc_final: 0.7943 (m-10) REVERT: E 304 ASN cc_start: 0.7996 (m110) cc_final: 0.7636 (m-40) REVERT: E 324 LYS cc_start: 0.8360 (mtmp) cc_final: 0.7679 (mtmm) REVERT: E 338 THR cc_start: 0.8528 (m) cc_final: 0.8191 (t) REVERT: E 340 LYS cc_start: 0.7711 (tttt) cc_final: 0.7413 (ttmt) REVERT: F 8 GLU cc_start: 0.7301 (tp30) cc_final: 0.6995 (tp30) REVERT: F 37 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7286 (mmtm) REVERT: F 57 SER cc_start: 0.8597 (p) cc_final: 0.8318 (t) REVERT: F 60 ASN cc_start: 0.7922 (m-40) cc_final: 0.7597 (m-40) REVERT: F 70 MET cc_start: 0.7448 (tpp) cc_final: 0.7182 (mmm) REVERT: F 75 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7737 (mmtp) REVERT: F 76 GLU cc_start: 0.6601 (tp30) cc_final: 0.6289 (tp30) REVERT: F 175 ASP cc_start: 0.8385 (t0) cc_final: 0.8021 (t0) REVERT: F 177 SER cc_start: 0.8738 (m) cc_final: 0.8404 (p) REVERT: F 261 LEU cc_start: 0.8514 (tp) cc_final: 0.8308 (mt) REVERT: F 290 LYS cc_start: 0.7739 (mttt) cc_final: 0.7474 (mttt) REVERT: H 38 ARG cc_start: 0.7233 (ptt-90) cc_final: 0.6849 (ptt-90) REVERT: H 40 SER cc_start: 0.8130 (p) cc_final: 0.7520 (t) REVERT: H 83 LYS cc_start: 0.8349 (tmtt) cc_final: 0.7994 (tptp) REVERT: L 20 THR cc_start: 0.8635 (t) cc_final: 0.8305 (p) REVERT: L 42 LYS cc_start: 0.8256 (mmmt) cc_final: 0.8052 (mmmt) REVERT: L 104 VAL cc_start: 0.8122 (t) cc_final: 0.7894 (p) outliers start: 64 outliers final: 46 residues processed: 709 average time/residue: 0.3515 time to fit residues: 361.2575 Evaluate side-chains 727 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 676 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 340 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 81 GLN Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 82 VAL 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 255 LEU Chi-restraints excluded: chain D residue 257 VAL 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 318 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 0.0170 chunk 80 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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 C 270 ASN ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 349 GLN ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103250 restraints weight = 31038.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106324 restraints weight = 13545.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108145 restraints weight = 7206.073| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19647 Z= 0.218 Angle : 0.620 9.662 26742 Z= 0.319 Chirality : 0.045 0.170 2935 Planarity : 0.004 0.039 3462 Dihedral : 4.974 23.028 2674 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.09 % Allowed : 19.99 % 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: -1.62 (0.17), residues: 2445 helix: -1.73 (0.67), residues: 49 sheet: -0.31 (0.17), residues: 871 loop : -1.58 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.005 0.001 HIS D 168 PHE 0.018 0.001 PHE D 338 TYR 0.031 0.001 TYR F 9 ARG 0.003 0.000 ARG D 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6144.47 seconds wall clock time: 112 minutes 9.80 seconds (6729.80 seconds total)