Starting phenix.real_space_refine on Sun Aug 9 04:45:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yb1_72745/08_2026/9yb1_72745.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yb1_72745/08_2026/9yb1_72745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yb1_72745/08_2026/9yb1_72745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yb1_72745/08_2026/9yb1_72745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yb1_72745/08_2026/9yb1_72745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yb1_72745/08_2026/9yb1_72745.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.038 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 204 5.16 5 C 20059 2.51 5 N 5490 2.21 5 O 5926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31679 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3329 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 407} Chain: "B" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3329 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 407} Chain: "C" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3329 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 407} Chain: "D" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3329 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 407} Chain: "P" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1239 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "Q" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1239 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "R" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1230 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "S" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1239 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "a" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3301 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "b" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3301 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "c" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3301 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "d" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3301 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 387} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.15, per 1000 atoms: 0.23 Number of scatterers: 31679 At special positions: 0 Unit cell: (162.26, 171.57, 202.16, 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 204 16.00 O 5926 8.00 N 5490 7.00 C 20059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.01 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.05 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.01 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.01 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.02 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 272 " distance=2.04 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 371 " distance=2.02 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.01 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.04 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 260 " - pdb=" SG CYS C 272 " distance=2.05 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 377 " distance=2.01 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 371 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.02 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.02 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.03 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.02 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS a 122 " distance=2.04 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 27 " distance=2.02 Simple disulfide: pdb=" SG CYS a 89 " - pdb=" SG CYS a 103 " distance=2.02 Simple disulfide: pdb=" SG CYS a 150 " - pdb=" SG CYS a 263 " distance=2.03 Simple disulfide: pdb=" SG CYS a 199 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 201 " - pdb=" SG CYS a 217 " distance=2.03 Simple disulfide: pdb=" SG CYS b 19 " - pdb=" SG CYS b 122 " distance=2.02 Simple disulfide: pdb=" SG CYS b 22 " - pdb=" SG CYS b 27 " distance=2.02 Simple disulfide: pdb=" SG CYS b 89 " - pdb=" SG CYS b 103 " distance=2.01 Simple disulfide: pdb=" SG CYS b 150 " - pdb=" SG CYS b 263 " distance=2.03 Simple disulfide: pdb=" SG CYS b 199 " - pdb=" SG CYS b 223 " distance=2.01 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 217 " distance=2.03 Simple disulfide: pdb=" SG CYS c 19 " - pdb=" SG CYS c 122 " distance=2.02 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 27 " distance=2.02 Simple disulfide: pdb=" SG CYS c 89 " - pdb=" SG CYS c 103 " distance=2.02 Simple disulfide: pdb=" SG CYS c 150 " - pdb=" SG CYS c 263 " distance=2.02 Simple disulfide: pdb=" SG CYS c 199 " - pdb=" SG CYS c 223 " distance=2.04 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 217 " distance=2.02 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS d 122 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 27 " distance=2.02 Simple disulfide: pdb=" SG CYS d 89 " - pdb=" SG CYS d 103 " distance=2.03 Simple disulfide: pdb=" SG CYS d 150 " - pdb=" SG CYS d 263 " distance=2.03 Simple disulfide: pdb=" SG CYS d 199 " - pdb=" SG CYS d 223 " distance=2.04 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 217 " distance=2.01 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG b 501 " - " ASN b 315 " " NAG c 501 " - " ASN c 315 " " NAG d 501 " - " ASN d 315 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7518 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 93 sheets defined 14.8% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 removed outlier: 4.224A pdb=" N ILE A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 404 through 428 removed outlier: 3.797A pdb=" N SER A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TRP A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 225 through 229 removed outlier: 4.335A pdb=" N GLY B 228 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 248 removed outlier: 3.696A pdb=" N ARG B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Proline residue: B 257 - end of helix Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 404 through 427 removed outlier: 4.331A pdb=" N LEU B 414 " --> pdb=" O TRP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 4.223A pdb=" N VAL B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 99 removed outlier: 3.503A pdb=" N GLU C 99 " --> pdb=" O CYS C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 99' Processing helix chain 'C' and resid 111 through 116 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.800A pdb=" N GLY C 259 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS C 260 " --> pdb=" O PRO C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 260' Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 396 through 402 removed outlier: 4.346A pdb=" N PHE C 399 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 428 removed outlier: 3.758A pdb=" N LYS C 412 " --> pdb=" O TRP C 408 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU C 414 " --> pdb=" O TRP C 410 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 437 removed outlier: 3.692A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 432 through 437' Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 239 through 247 removed outlier: 3.511A pdb=" N LYS D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 407 through 428 removed outlier: 4.930A pdb=" N VAL D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU D 414 " --> pdb=" O TRP D 410 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 437 removed outlier: 3.576A pdb=" N PHE D 437 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 111 removed outlier: 3.631A pdb=" N ASP P 111 " --> pdb=" O LYS P 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 150 Processing helix chain 'P' and resid 157 through 159 No H-bonds generated for 'chain 'P' and resid 157 through 159' Processing helix chain 'P' and resid 167 through 171 Processing helix chain 'Q' and resid 103 through 111 removed outlier: 4.351A pdb=" N LEU Q 108 " --> pdb=" O MET Q 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP Q 111 " --> pdb=" O LYS Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 151 removed outlier: 3.645A pdb=" N ILE Q 151 " --> pdb=" O GLN Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 171 Processing helix chain 'R' and resid 104 through 111 removed outlier: 3.701A pdb=" N LEU R 108 " --> pdb=" O MET R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 150 Processing helix chain 'R' and resid 157 through 159 No H-bonds generated for 'chain 'R' and resid 157 through 159' Processing helix chain 'S' and resid 103 through 110 Processing helix chain 'S' and resid 145 through 150 removed outlier: 3.673A pdb=" N ALA S 150 " --> pdb=" O GLU S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 160 Processing helix chain 'S' and resid 167 through 172 removed outlier: 3.636A pdb=" N SER S 172 " --> pdb=" O GLN S 168 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 212 removed outlier: 4.051A pdb=" N ASP S 211 " --> pdb=" O GLY S 207 " (cutoff:3.500A) Processing helix chain 'a' and resid 1 through 4 Processing helix chain 'a' and resid 5 through 12 Processing helix chain 'a' and resid 219 through 223 Processing helix chain 'a' and resid 350 through 352 No H-bonds generated for 'chain 'a' and resid 350 through 352' Processing helix chain 'a' and resid 353 through 360 removed outlier: 3.700A pdb=" N TYR a 357 " --> pdb=" O VAL a 353 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR a 360 " --> pdb=" O TYR a 356 " (cutoff:3.500A) Processing helix chain 'a' and resid 360 through 392 removed outlier: 4.619A pdb=" N ILE a 366 " --> pdb=" O LEU a 362 " (cutoff:3.500A) Processing helix chain 'a' and resid 394 through 400 removed outlier: 3.570A pdb=" N ALA a 400 " --> pdb=" O PRO a 396 " (cutoff:3.500A) Processing helix chain 'a' and resid 406 through 412 removed outlier: 3.720A pdb=" N ALA a 410 " --> pdb=" O PRO a 406 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 12 removed outlier: 3.835A pdb=" N THR b 7 " --> pdb=" O ASP b 3 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN b 8 " --> pdb=" O THR b 4 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR b 9 " --> pdb=" O HIS b 5 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA b 12 " --> pdb=" O GLN b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 79 through 81 No H-bonds generated for 'chain 'b' and resid 79 through 81' Processing helix chain 'b' and resid 348 through 353 Processing helix chain 'b' and resid 353 through 358 Processing helix chain 'b' and resid 362 through 392 removed outlier: 3.801A pdb=" N CYS b 369 " --> pdb=" O ILE b 365 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU b 392 " --> pdb=" O ARG b 388 " (cutoff:3.500A) Processing helix chain 'b' and resid 406 through 412 removed outlier: 3.720A pdb=" N ALA b 410 " --> pdb=" O PRO b 406 " (cutoff:3.500A) Processing helix chain 'c' and resid 1 through 5 removed outlier: 3.549A pdb=" N THR c 4 " --> pdb=" O ASP c 1 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 Processing helix chain 'c' and resid 79 through 81 No H-bonds generated for 'chain 'c' and resid 79 through 81' Processing helix chain 'c' and resid 174 through 176 No H-bonds generated for 'chain 'c' and resid 174 through 176' Processing helix chain 'c' and resid 348 through 360 removed outlier: 3.790A pdb=" N VAL c 354 " --> pdb=" O HIS c 350 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR c 355 " --> pdb=" O GLU c 351 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR c 360 " --> pdb=" O TYR c 356 " (cutoff:3.500A) Processing helix chain 'c' and resid 360 through 392 removed outlier: 4.071A pdb=" N ILE c 365 " --> pdb=" O PRO c 361 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE c 366 " --> pdb=" O LEU c 362 " (cutoff:3.500A) Processing helix chain 'c' and resid 394 through 399 removed outlier: 4.121A pdb=" N LEU c 399 " --> pdb=" O THR c 395 " (cutoff:3.500A) Processing helix chain 'c' and resid 406 through 410 removed outlier: 4.157A pdb=" N LEU c 409 " --> pdb=" O PRO c 406 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 4 No H-bonds generated for 'chain 'd' and resid 2 through 4' Processing helix chain 'd' and resid 5 through 12 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 364 through 392 Processing helix chain 'd' and resid 408 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 48 removed outlier: 5.489A pdb=" N THR A 42 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N HIS A 125 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS A 123 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 178 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA7, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA8, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 306 removed outlier: 3.779A pdb=" N GLU A 301 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 317 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 347 removed outlier: 3.958A pdb=" N VAL A 345 " --> pdb=" O CYS A 329 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 329 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 327 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.816A pdb=" N LYS B 161 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.671A pdb=" N MET B 132 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR B 36 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLN B 130 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 48 removed outlier: 3.623A pdb=" N SER B 41 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 121 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 178 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AB8, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB9, first strand: chain 'B' and resid 301 through 307 removed outlier: 5.818A pdb=" N CYS B 302 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 320 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE B 304 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N THR B 318 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 344 through 347 Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AC3, first strand: chain 'C' and resid 14 through 19 removed outlier: 6.477A pdb=" N MET C 132 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR C 36 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN C 130 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 133 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 145 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.931A pdb=" N ALA C 121 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 178 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 52 through 54 removed outlier: 3.973A pdb=" N THR C 101 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 61 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AC7, first strand: chain 'C' and resid 205 through 206 Processing sheet with id=AC8, first strand: chain 'C' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AD1, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.534A pdb=" N PHE C 353 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 319 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE C 316 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 301 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N LYS C 382 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS C 307 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 344 through 347 removed outlier: 3.789A pdb=" N VAL C 345 " --> pdb=" O CYS C 329 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 366 through 367 Processing sheet with id=AD4, first strand: chain 'D' and resid 3 through 8 removed outlier: 3.504A pdb=" N ILE D 281 " --> pdb=" O HIS D 3 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 15 through 18 removed outlier: 4.880A pdb=" N ILE D 31 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU D 33 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN D 134 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 145 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 41 through 48 removed outlier: 6.820A pdb=" N ALA D 121 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.565A pdb=" N TYR D 107 " --> pdb=" O LYS D 54 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AD9, first strand: chain 'D' and resid 204 through 205 Processing sheet with id=AE1, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AE2, first strand: chain 'D' and resid 261 through 262 removed outlier: 4.040A pdb=" N SER D 261 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 301 through 307 removed outlier: 6.185A pdb=" N CYS D 302 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA D 320 " --> pdb=" O CYS D 302 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE D 304 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N THR D 318 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AE5, first strand: chain 'P' and resid 121 through 126 removed outlier: 5.153A pdb=" N VAL P 122 " --> pdb=" O LEU P 118 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU P 118 " --> pdb=" O VAL P 122 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY P 124 " --> pdb=" O ILE P 116 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 128 through 129 removed outlier: 3.609A pdb=" N GLY P 164 " --> pdb=" O VAL P 133 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS P 135 " --> pdb=" O GLU P 162 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS P 154 " --> pdb=" O TYR P 163 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 186 through 188 Processing sheet with id=AE8, first strand: chain 'P' and resid 201 through 203 removed outlier: 3.694A pdb=" N ARG P 236 " --> pdb=" O GLU P 233 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 215 through 217 removed outlier: 6.792A pdb=" N ILE P 216 " --> pdb=" O VAL P 224 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL P 227 " --> pdb=" O VAL P 242 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL P 242 " --> pdb=" O VAL P 227 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 121 through 126 removed outlier: 6.990A pdb=" N ILE Q 116 " --> pdb=" O ASN Q 123 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR Q 125 " --> pdb=" O PHE Q 114 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE Q 114 " --> pdb=" O TYR Q 125 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 155 through 156 Processing sheet with id=AF3, first strand: chain 'Q' and resid 191 through 193 removed outlier: 3.701A pdb=" N ASN Q 187 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA Q 225 " --> pdb=" O ILE Q 216 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA Q 225 " --> pdb=" O TRP Q 244 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N TRP Q 244 " --> pdb=" O ALA Q 225 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL Q 227 " --> pdb=" O VAL Q 242 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL Q 242 " --> pdb=" O VAL Q 227 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 121 through 126 removed outlier: 4.827A pdb=" N VAL R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU R 118 " --> pdb=" O VAL R 122 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 128 through 129 removed outlier: 3.510A pdb=" N LEU R 161 " --> pdb=" O ALA R 156 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 191 through 193 removed outlier: 6.491A pdb=" N ILE R 216 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ALA R 225 " --> pdb=" O TRP R 244 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TRP R 244 " --> pdb=" O ALA R 225 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL R 227 " --> pdb=" O VAL R 242 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL R 242 " --> pdb=" O VAL R 227 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 142 through 143 removed outlier: 6.382A pdb=" N LEU S 118 " --> pdb=" O VAL S 122 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL S 122 " --> pdb=" O LEU S 118 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS S 127 " --> pdb=" O PHE S 134 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 187 through 188 Processing sheet with id=AF9, first strand: chain 'S' and resid 202 through 203 removed outlier: 3.880A pdb=" N VAL S 202 " --> pdb=" O THR S 237 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 215 through 217 removed outlier: 6.950A pdb=" N ILE S 216 " --> pdb=" O VAL S 224 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N VAL S 224 " --> pdb=" O TRP S 244 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TRP S 244 " --> pdb=" O VAL S 224 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 17 through 22 removed outlier: 3.502A pdb=" N CYS a 27 " --> pdb=" O CYS a 19 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN a 21 " --> pdb=" O SER a 25 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER a 25 " --> pdb=" O ASN a 21 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 33 through 37 removed outlier: 5.004A pdb=" N GLU a 35 " --> pdb=" O GLN a 48 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN a 48 " --> pdb=" O GLU a 35 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA a 101 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN a 102 " --> pdb=" O LEU a 91 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU a 91 " --> pdb=" O GLN a 102 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 67 through 69 Processing sheet with id=AG5, first strand: chain 'a' and resid 82 through 84 removed outlier: 4.366A pdb=" N ASP a 107 " --> pdb=" O HIS a 126 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 146 through 149 Processing sheet with id=AG7, first strand: chain 'a' and resid 152 through 153 Processing sheet with id=AG8, first strand: chain 'a' and resid 234 through 235 Processing sheet with id=AG9, first strand: chain 'a' and resid 172 through 173 Processing sheet with id=AH1, first strand: chain 'a' and resid 272 through 274 Processing sheet with id=AH2, first strand: chain 'a' and resid 304 through 308 Processing sheet with id=AH3, first strand: chain 'b' and resid 44 through 53 removed outlier: 11.692A pdb=" N ILE b 47 " --> pdb=" O GLN b 102 " (cutoff:3.500A) removed outlier: 11.654A pdb=" N GLN b 102 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 12.289A pdb=" N THR b 49 " --> pdb=" O LEU b 100 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N LEU b 100 " --> pdb=" O THR b 49 " (cutoff:3.500A) removed outlier: 10.555A pdb=" N ALA b 51 " --> pdb=" O TYR b 98 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR b 98 " --> pdb=" O ALA b 51 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 64 through 68 Processing sheet with id=AH5, first strand: chain 'b' and resid 82 through 84 removed outlier: 4.365A pdb=" N ASP b 107 " --> pdb=" O HIS b 126 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 146 through 153 Processing sheet with id=AH7, first strand: chain 'b' and resid 234 through 235 Processing sheet with id=AH8, first strand: chain 'b' and resid 172 through 173 removed outlier: 3.743A pdb=" N VAL b 172 " --> pdb=" O LEU b 227 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'b' and resid 178 through 180 Processing sheet with id=AI1, first strand: chain 'b' and resid 272 through 276 removed outlier: 3.703A pdb=" N LEU b 284 " --> pdb=" O THR b 312 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR b 312 " --> pdb=" O LEU b 284 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 304 through 308 removed outlier: 3.660A pdb=" N THR b 304 " --> pdb=" O THR b 294 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'c' and resid 25 through 27 removed outlier: 5.492A pdb=" N SER c 25 " --> pdb=" O ASN c 21 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN c 21 " --> pdb=" O SER c 25 " (cutoff:3.500A) removed outlier: 13.023A pdb=" N CYS c 19 " --> pdb=" O ALA c 125 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N ALA c 125 " --> pdb=" O CYS c 19 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN c 21 " --> pdb=" O THR c 123 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS c 122 " --> pdb=" O GLY c 112 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLY c 112 " --> pdb=" O CYS c 122 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL c 124 " --> pdb=" O THR c 110 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N THR c 110 " --> pdb=" O VAL c 124 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N HIS c 126 " --> pdb=" O THR c 108 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR c 108 " --> pdb=" O HIS c 126 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'c' and resid 33 through 37 removed outlier: 8.182A pdb=" N ILE c 33 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER c 50 " --> pdb=" O ILE c 33 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU c 35 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN c 48 " --> pdb=" O GLU c 35 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG c 37 " --> pdb=" O ARG c 46 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N SER c 50 " --> pdb=" O MET c 68 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET c 68 " --> pdb=" O SER c 50 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'c' and resid 33 through 37 removed outlier: 8.182A pdb=" N ILE c 33 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER c 50 " --> pdb=" O ILE c 33 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU c 35 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN c 48 " --> pdb=" O GLU c 35 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG c 37 " --> pdb=" O ARG c 46 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR c 97 " --> pdb=" O THR c 49 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ALA c 51 " --> pdb=" O HIS c 95 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N HIS c 95 " --> pdb=" O ALA c 51 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N PHE c 53 " --> pdb=" O SER c 93 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N SER c 93 " --> pdb=" O PHE c 53 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'c' and resid 146 through 153 Processing sheet with id=AI7, first strand: chain 'c' and resid 234 through 235 Processing sheet with id=AI8, first strand: chain 'c' and resid 178 through 179 Processing sheet with id=AI9, first strand: chain 'c' and resid 272 through 276 removed outlier: 3.537A pdb=" N PHE c 316 " --> pdb=" O LEU c 280 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'c' and resid 304 through 308 removed outlier: 3.504A pdb=" N THR c 304 " --> pdb=" O THR c 294 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU c 323 " --> pdb=" O VAL c 335 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'd' and resid 17 through 22 removed outlier: 3.757A pdb=" N ALA d 17 " --> pdb=" O SER d 29 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN d 21 " --> pdb=" O SER d 25 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER d 25 " --> pdb=" O ASN d 21 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 33 through 37 removed outlier: 5.106A pdb=" N GLU d 35 " --> pdb=" O GLN d 48 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR d 98 " --> pdb=" O HIS d 94 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N HIS d 94 " --> pdb=" O TYR d 98 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU d 100 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'd' and resid 52 through 53 removed outlier: 3.828A pdb=" N MET d 52 " --> pdb=" O SER d 66 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'd' and resid 82 through 84 Processing sheet with id=AJ6, first strand: chain 'd' and resid 146 through 153 Processing sheet with id=AJ7, first strand: chain 'd' and resid 163 through 165 Processing sheet with id=AJ8, first strand: chain 'd' and resid 172 through 173 Processing sheet with id=AJ9, first strand: chain 'd' and resid 178 through 179 Processing sheet with id=AK1, first strand: chain 'd' and resid 198 through 199 Processing sheet with id=AK2, first strand: chain 'd' and resid 272 through 276 Processing sheet with id=AK3, first strand: chain 'd' and resid 304 through 308 932 hydrogen bonds defined for protein. 2238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5443 1.30 - 1.43: 8463 1.43 - 1.56: 18365 1.56 - 1.69: 0 1.69 - 1.82: 256 Bond restraints: 32527 Sorted by residual: bond pdb=" CA ALA C 106 " pdb=" CB ALA C 106 " ideal model delta sigma weight residual 1.532 1.451 0.081 1.68e-02 3.54e+03 2.34e+01 bond pdb=" CE1 HIS B 363 " pdb=" NE2 HIS B 363 " ideal model delta sigma weight residual 1.321 1.274 0.047 1.00e-02 1.00e+04 2.18e+01 bond pdb=" CE LYS c 56 " pdb=" NZ LYS c 56 " ideal model delta sigma weight residual 1.489 1.349 0.140 3.00e-02 1.11e+03 2.18e+01 bond pdb=" CB THR d 418 " pdb=" OG1 THR d 418 " ideal model delta sigma weight residual 1.433 1.362 0.071 1.60e-02 3.91e+03 1.97e+01 bond pdb=" CE LYS B 50 " pdb=" NZ LYS B 50 " ideal model delta sigma weight residual 1.489 1.358 0.131 3.00e-02 1.11e+03 1.91e+01 ... (remaining 32522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 33981 1.80 - 3.60: 8826 3.60 - 5.40: 1337 5.40 - 7.20: 182 7.20 - 9.00: 14 Bond angle restraints: 44340 Sorted by residual: angle pdb=" N PRO D 383 " pdb=" CA PRO D 383 " pdb=" CB PRO D 383 " ideal model delta sigma weight residual 103.19 106.52 -3.33 5.60e-01 3.19e+00 3.54e+01 angle pdb=" CA HIS C 387 " pdb=" CB HIS C 387 " pdb=" CG HIS C 387 " ideal model delta sigma weight residual 113.80 119.63 -5.83 1.00e+00 1.00e+00 3.40e+01 angle pdb=" N SER D 404 " pdb=" CA SER D 404 " pdb=" C SER D 404 " ideal model delta sigma weight residual 113.16 106.00 7.16 1.24e+00 6.50e-01 3.34e+01 angle pdb=" OD1 ASN a 80 " pdb=" CG ASN a 80 " pdb=" ND2 ASN a 80 " ideal model delta sigma weight residual 122.60 116.99 5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" N LYS D 412 " pdb=" CA LYS D 412 " pdb=" C LYS D 412 " ideal model delta sigma weight residual 111.71 105.35 6.36 1.15e+00 7.56e-01 3.06e+01 ... (remaining 44335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 18276 21.26 - 42.52: 1137 42.52 - 63.77: 253 63.77 - 85.03: 38 85.03 - 106.29: 22 Dihedral angle restraints: 19726 sinusoidal: 7977 harmonic: 11749 Sorted by residual: dihedral pdb=" CA TYR d 360 " pdb=" C TYR d 360 " pdb=" N PRO d 361 " pdb=" CA PRO d 361 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASN d 358 " pdb=" C ASN d 358 " pdb=" N ARG d 359 " pdb=" CA ARG d 359 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ARG a 37 " pdb=" C ARG a 37 " pdb=" N GLY a 38 " pdb=" CA GLY a 38 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 19723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3765 0.095 - 0.191: 1011 0.191 - 0.286: 181 0.286 - 0.381: 20 0.381 - 0.477: 9 Chirality restraints: 4986 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.71e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.69e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.69e+02 ... (remaining 4983 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN c 315 " 0.176 2.00e-02 2.50e+03 2.52e-01 7.96e+02 pdb=" CG ASN c 315 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN c 315 " 0.035 2.00e-02 2.50e+03 pdb=" ND2 ASN c 315 " -0.437 2.00e-02 2.50e+03 pdb=" C1 NAG c 501 " 0.300 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN d 315 " 0.179 2.00e-02 2.50e+03 2.37e-01 7.04e+02 pdb=" CG ASN d 315 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN d 315 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN d 315 " -0.403 2.00e-02 2.50e+03 pdb=" C1 NAG d 501 " 0.285 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 501 " 0.271 2.00e-02 2.50e+03 2.29e-01 6.57e+02 pdb=" C7 NAG d 501 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG d 501 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG d 501 " -0.394 2.00e-02 2.50e+03 pdb=" O7 NAG d 501 " 0.020 2.00e-02 2.50e+03 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 10 2.41 - 3.03: 19819 3.03 - 3.65: 50519 3.65 - 4.28: 69757 4.28 - 4.90: 110158 Nonbonded interactions: 250263 Sorted by model distance: nonbonded pdb=" OD1 ASN A 134 " pdb=" C1 NAG E 1 " model vdw 1.784 3.470 nonbonded pdb=" CE2 TYR d 397 " pdb=" O ALA d 403 " model vdw 2.220 3.340 nonbonded pdb=" CB ALA S 156 " pdb=" NZ LYS d 398 " model vdw 2.271 3.540 nonbonded pdb=" O ILE c 407 " pdb=" N LEU c 411 " model vdw 2.330 3.120 nonbonded pdb=" O ILE c 415 " pdb=" C LYS c 416 " model vdw 2.353 3.270 ... (remaining 250258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'P' and resid 103 through 261) selection = (chain 'Q' and resid 103 through 261) selection = chain 'R' selection = (chain 'S' and resid 103 through 261) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 0.780 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 29.420 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 0.536 32595 Z= 0.794 Angle : 1.608 12.303 44485 Z= 1.054 Chirality : 0.088 0.477 4986 Planarity : 0.016 0.285 5694 Dihedral : 15.163 106.291 12040 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.30 % Favored : 90.21 % Rotamer: Outliers : 10.70 % Allowed : 12.52 % Favored : 76.78 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.12), residues: 4043 helix: -0.35 (0.26), residues: 403 sheet: -1.79 (0.17), residues: 877 loop : -1.81 (0.11), residues: 2763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 143 TYR 0.222 0.020 TYR B 391 PHE 0.073 0.012 PHE A 399 TRP 0.159 0.023 TRP D 89 HIS 0.024 0.005 HIS c 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01209 / 0.74 (32527) covalent geometry : angle 1.59959 / 1.05 (44340) SS BOND : bond 0.01104 / 0.74 ( 56) SS BOND : angle 1.90610 / 1.36 ( 112) hydrogen bonds : bond 0.18493 / 12.14 ( 919) hydrogen bonds : angle 10.65297 / 7.23 ( 2238) Misc. bond : bond 0.53640 / 28.23 ( 1) link_BETA1-4 : bond 0.04502 / 2.33 ( 8) link_BETA1-4 : angle 6.74461 / 4.01 ( 24) link_NAG-ASN : bond 0.00808 / 0.41 ( 3) link_NAG-ASN : angle 3.02160 / 1.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 371 poor density : 1074 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 18 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6370 (pp) REVERT: A 47 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8805 (tp) REVERT: A 103 MET cc_start: 0.9262 (ttt) cc_final: 0.8804 (ttp) REVERT: A 120 LYS cc_start: 0.9714 (mttt) cc_final: 0.9469 (mtmm) REVERT: A 132 MET cc_start: 0.9371 (mtp) cc_final: 0.8703 (tpt) REVERT: A 134 ASN cc_start: 0.5953 (OUTLIER) cc_final: 0.4916 (t0) REVERT: A 143 ARG cc_start: 0.9304 (ttm-80) cc_final: 0.8856 (ttp80) REVERT: A 245 LYS cc_start: 0.9492 (tptm) cc_final: 0.8984 (mmmt) REVERT: A 268 ARG cc_start: 0.9056 (ttp-170) cc_final: 0.8830 (mtm110) REVERT: A 271 ASN cc_start: 0.8936 (m110) cc_final: 0.8505 (m-40) REVERT: A 347 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8453 (pp) REVERT: A 353 PHE cc_start: 0.9243 (t80) cc_final: 0.8991 (t80) REVERT: A 394 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: A 396 THR cc_start: 0.8895 (t) cc_final: 0.8615 (p) REVERT: B 15 TYR cc_start: 0.9170 (t80) cc_final: 0.8699 (t80) REVERT: B 16 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8750 (tptp) REVERT: B 85 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8820 (t80) REVERT: B 99 GLU cc_start: 0.9841 (mm-30) cc_final: 0.9562 (mp0) REVERT: B 130 GLN cc_start: 0.9431 (OUTLIER) cc_final: 0.9196 (pp30) REVERT: B 142 TRP cc_start: 0.8104 (p-90) cc_final: 0.7584 (p-90) REVERT: B 207 ARG cc_start: 0.9524 (mmt90) cc_final: 0.9220 (mmp-170) REVERT: B 234 PHE cc_start: 0.8961 (p90) cc_final: 0.8680 (p90) REVERT: B 245 LYS cc_start: 0.9630 (mtpp) cc_final: 0.9196 (mmtm) REVERT: B 247 ASP cc_start: 0.9634 (t70) cc_final: 0.9285 (t70) REVERT: B 271 ASN cc_start: 0.9438 (m110) cc_final: 0.9114 (t0) REVERT: B 366 PHE cc_start: 0.9045 (p90) cc_final: 0.8712 (p90) REVERT: B 368 LEU cc_start: 0.9657 (tp) cc_final: 0.9444 (tp) REVERT: B 382 LYS cc_start: 0.9873 (OUTLIER) cc_final: 0.9672 (mmtm) REVERT: B 437 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.8932 (p90) REVERT: C 45 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9114 (mm-30) REVERT: C 52 LYS cc_start: 0.9302 (pttm) cc_final: 0.8429 (pttt) REVERT: C 85 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8248 (t80) REVERT: C 97 ASP cc_start: 0.9671 (m-30) cc_final: 0.9432 (m-30) REVERT: C 125 HIS cc_start: 0.9492 (m90) cc_final: 0.9264 (m90) REVERT: C 192 GLU cc_start: 0.9478 (mt-10) cc_final: 0.9199 (mp0) REVERT: C 243 ARG cc_start: 0.9370 (mtp180) cc_final: 0.8677 (mtp-110) REVERT: C 255 VAL cc_start: 0.9675 (OUTLIER) cc_final: 0.9417 (m) REVERT: C 268 ARG cc_start: 0.8773 (ttt180) cc_final: 0.8548 (tmm-80) REVERT: C 304 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.8942 (tp) REVERT: D 54 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8593 (tptp) REVERT: D 79 GLN cc_start: 0.9693 (mm-40) cc_final: 0.9488 (tm-30) REVERT: D 124 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8372 (p) REVERT: D 291 ILE cc_start: 0.9678 (OUTLIER) cc_final: 0.9377 (mt) REVERT: D 362 ILE cc_start: 0.9637 (tt) cc_final: 0.9400 (tp) REVERT: D 434 LEU cc_start: 0.9357 (tp) cc_final: 0.9106 (pp) REVERT: P 121 GLN cc_start: 0.9590 (tp-100) cc_final: 0.9362 (tm-30) REVERT: P 122 VAL cc_start: 0.9739 (OUTLIER) cc_final: 0.9072 (t) REVERT: P 159 TYR cc_start: 0.9564 (m-80) cc_final: 0.9181 (m-80) REVERT: P 162 GLU cc_start: 0.9458 (tt0) cc_final: 0.9243 (tt0) REVERT: P 195 TYR cc_start: 0.8172 (t80) cc_final: 0.7800 (t80) REVERT: P 209 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9293 (mttm) REVERT: P 253 ASP cc_start: 0.9093 (t0) cc_final: 0.8831 (t0) REVERT: Q 135 LYS cc_start: 0.9504 (pttt) cc_final: 0.9301 (ptmm) REVERT: Q 140 GLU cc_start: 0.9232 (pm20) cc_final: 0.8932 (mp0) REVERT: Q 153 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7586 (pp) REVERT: Q 157 SER cc_start: 0.9753 (p) cc_final: 0.9484 (p) REVERT: Q 161 LEU cc_start: 0.9873 (OUTLIER) cc_final: 0.9615 (mm) REVERT: Q 169 CYS cc_start: 0.9571 (m) cc_final: 0.9325 (m) REVERT: Q 196 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8967 (mp0) REVERT: Q 199 ARG cc_start: 0.9266 (ptp90) cc_final: 0.8933 (ptp-110) REVERT: Q 219 ASN cc_start: 0.9294 (p0) cc_final: 0.8575 (p0) REVERT: Q 228 LEU cc_start: 0.9547 (tp) cc_final: 0.9281 (tt) REVERT: Q 239 LEU cc_start: 0.9374 (mt) cc_final: 0.8999 (mt) REVERT: Q 244 TRP cc_start: 0.8848 (m-90) cc_final: 0.8261 (m-90) REVERT: R 127 CYS cc_start: 0.8460 (p) cc_final: 0.8158 (p) REVERT: R 199 ARG cc_start: 0.9115 (ptt-90) cc_final: 0.8676 (ptp90) REVERT: R 247 LYS cc_start: 0.9663 (mmmm) cc_final: 0.9310 (tptp) REVERT: S 147 GLN cc_start: 0.9601 (OUTLIER) cc_final: 0.9279 (tm-30) REVERT: S 160 ASP cc_start: 0.9216 (OUTLIER) cc_final: 0.8929 (p0) REVERT: S 198 ASN cc_start: 0.9305 (m110) cc_final: 0.8859 (p0) REVERT: S 199 ARG cc_start: 0.9562 (mmt-90) cc_final: 0.9096 (mmm160) REVERT: a 16 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7694 (mp) REVERT: a 53 PHE cc_start: 0.9590 (m-80) cc_final: 0.8868 (m-80) REVERT: a 64 TYR cc_start: 0.9530 (m-80) cc_final: 0.9295 (m-80) REVERT: a 114 HIS cc_start: 0.9267 (OUTLIER) cc_final: 0.8594 (m-70) REVERT: a 129 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8174 (mt-10) REVERT: a 200 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8331 (tmmt) REVERT: a 240 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8691 (mm) REVERT: a 267 LEU cc_start: 0.9442 (tp) cc_final: 0.9013 (mt) REVERT: a 280 LEU cc_start: 0.9123 (tp) cc_final: 0.8915 (tp) REVERT: a 287 ASP cc_start: 0.8621 (p0) cc_final: 0.8237 (p0) REVERT: a 358 ASN cc_start: 0.9343 (OUTLIER) cc_final: 0.9065 (p0) REVERT: a 391 ASN cc_start: 0.9268 (t0) cc_final: 0.9034 (m-40) REVERT: b 6 PHE cc_start: 0.9235 (t80) cc_final: 0.8358 (t80) REVERT: b 47 ILE cc_start: 0.9708 (mt) cc_final: 0.9409 (tp) REVERT: b 52 MET cc_start: 0.9594 (mpt) cc_final: 0.9372 (mpt) REVERT: b 97 TYR cc_start: 0.9286 (p90) cc_final: 0.8819 (p90) REVERT: b 120 HIS cc_start: 0.9131 (m170) cc_final: 0.8116 (m170) REVERT: b 185 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7634 (p) REVERT: b 198 TYR cc_start: 0.9473 (t80) cc_final: 0.9236 (t80) REVERT: b 205 ARG cc_start: 0.8824 (ttm110) cc_final: 0.8521 (mmt90) REVERT: b 272 LEU cc_start: 0.9654 (tp) cc_final: 0.9408 (tp) REVERT: b 281 ILE cc_start: 0.9624 (OUTLIER) cc_final: 0.9251 (pt) REVERT: b 283 HIS cc_start: 0.9617 (m170) cc_final: 0.9077 (m170) REVERT: c 68 MET cc_start: 0.9516 (mmm) cc_final: 0.9217 (tpp) REVERT: c 73 GLN cc_start: 0.9739 (pt0) cc_final: 0.9327 (pp30) REVERT: c 97 TYR cc_start: 0.8340 (m-80) cc_final: 0.7728 (m-80) REVERT: c 98 TYR cc_start: 0.9247 (m-80) cc_final: 0.8946 (m-80) REVERT: c 102 GLN cc_start: 0.9084 (pt0) cc_final: 0.8868 (pm20) REVERT: c 129 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8586 (mp0) REVERT: c 143 GLU cc_start: 0.9474 (OUTLIER) cc_final: 0.9207 (pp20) REVERT: c 144 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8232 (p-80) REVERT: c 157 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8303 (mmp80) REVERT: c 167 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.8789 (p90) REVERT: c 194 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: c 275 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.8567 (t-90) REVERT: c 292 LEU cc_start: 0.9151 (tp) cc_final: 0.8931 (tp) REVERT: c 297 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8655 (mt) REVERT: c 305 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8829 (ttm170) REVERT: c 366 ILE cc_start: 0.9447 (mm) cc_final: 0.9166 (mt) REVERT: c 369 CYS cc_start: 0.9804 (t) cc_final: 0.9536 (p) REVERT: d 52 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9204 (ptm) REVERT: d 53 PHE cc_start: 0.8748 (m-80) cc_final: 0.8468 (m-80) REVERT: d 79 ASP cc_start: 0.8527 (p0) cc_final: 0.8054 (p0) REVERT: d 163 TYR cc_start: 0.8540 (p90) cc_final: 0.8269 (p90) REVERT: d 236 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: d 240 LEU cc_start: 0.9412 (mt) cc_final: 0.9183 (pp) REVERT: d 270 GLU cc_start: 0.9627 (tp30) cc_final: 0.9140 (tm-30) REVERT: d 275 HIS cc_start: 0.9272 (OUTLIER) cc_final: 0.8698 (p-80) REVERT: d 292 LEU cc_start: 0.9140 (tp) cc_final: 0.8394 (pp) REVERT: d 293 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8391 (p) REVERT: d 296 SER cc_start: 0.9461 (OUTLIER) cc_final: 0.9160 (p) REVERT: d 302 ASN cc_start: 0.9383 (m-40) cc_final: 0.9145 (m-40) REVERT: d 355 TYR cc_start: 0.8385 (m-80) cc_final: 0.7908 (m-80) REVERT: d 413 CYS cc_start: 0.9580 (t) cc_final: 0.9327 (m) outliers start: 371 outliers final: 121 residues processed: 1355 average time/residue: 0.2214 time to fit residues: 458.3124 Evaluate side-chains 809 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 646 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS A 219 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 102 GLN B 125 HIS ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 HIS C 363 HIS ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 130 GLN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN D 363 HIS P 147 GLN ** P 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 189 HIS ** S 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 ASN a 82 HIS ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 144 HIS a 162 HIS ** a 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 GLN b 82 HIS ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 213 HIS ** b 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 283 HIS ** b 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 5 HIS c 114 HIS c 167 HIS c 277 HIS ** c 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 338 GLN ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 GLN d 102 GLN ** d 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 HIS d 175 HIS ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 283 HIS ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 288 HIS ** d 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 346 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.051351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.038540 restraints weight = 238652.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.040212 restraints weight = 141767.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.041439 restraints weight = 98863.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.042331 restraints weight = 75598.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.043015 restraints weight = 61528.519| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32595 Z= 0.185 Angle : 0.792 19.771 44485 Z= 0.410 Chirality : 0.050 0.420 4986 Planarity : 0.006 0.070 5694 Dihedral : 8.378 85.575 4739 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.62 % Favored : 92.21 % Rotamer: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.13), residues: 4043 helix: -0.10 (0.25), residues: 453 sheet: -1.64 (0.16), residues: 963 loop : -1.57 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG d 224 TYR 0.055 0.003 TYR c 226 PHE 0.040 0.002 PHE Q 185 TRP 0.070 0.003 TRP D 410 HIS 0.017 0.002 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (32527) covalent geometry : angle 0.76951 / 0.40 (44340) SS BOND : bond 0.00460 / 0.29 ( 56) SS BOND : angle 1.61274 / 1.04 ( 112) hydrogen bonds : bond 0.05509 / 3.64 ( 919) hydrogen bonds : angle 8.76521 / 5.97 ( 2238) Misc. bond : bond 0.00643 / 0.34 ( 1) link_BETA1-4 : bond 0.01028 / 0.49 ( 8) link_BETA1-4 : angle 3.83271 / 2.25 ( 24) link_NAG-ASN : bond 0.01445 / 0.74 ( 3) link_NAG-ASN : angle 10.57560 / 6.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 852 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9427 (pm20) cc_final: 0.9097 (tm-30) REVERT: A 105 GLU cc_start: 0.8687 (pm20) cc_final: 0.8329 (pm20) REVERT: A 175 ASP cc_start: 0.9523 (m-30) cc_final: 0.9277 (p0) REVERT: A 213 ASP cc_start: 0.9531 (p0) cc_final: 0.9295 (t0) REVERT: A 214 LEU cc_start: 0.9321 (pp) cc_final: 0.9005 (mt) REVERT: A 215 TYR cc_start: 0.9253 (m-10) cc_final: 0.8845 (m-10) REVERT: A 234 PHE cc_start: 0.9456 (p90) cc_final: 0.9186 (p90) REVERT: A 244 TRP cc_start: 0.9621 (t60) cc_final: 0.9402 (t60) REVERT: A 268 ARG cc_start: 0.9015 (ttp-170) cc_final: 0.8522 (mtp-110) REVERT: B 15 TYR cc_start: 0.9431 (t80) cc_final: 0.8867 (t80) REVERT: B 103 MET cc_start: 0.9393 (ttt) cc_final: 0.9186 (tpp) REVERT: B 117 ASP cc_start: 0.9877 (t0) cc_final: 0.9571 (p0) REVERT: B 142 TRP cc_start: 0.8895 (p-90) cc_final: 0.8300 (p-90) REVERT: B 175 ASP cc_start: 0.9683 (m-30) cc_final: 0.9402 (p0) REVERT: B 188 TYR cc_start: 0.9163 (t80) cc_final: 0.8791 (t80) REVERT: B 242 GLU cc_start: 0.9830 (tt0) cc_final: 0.9584 (tm-30) REVERT: B 254 ASP cc_start: 0.9813 (m-30) cc_final: 0.9382 (t0) REVERT: B 356 HIS cc_start: 0.9716 (m-70) cc_final: 0.9498 (m90) REVERT: B 366 PHE cc_start: 0.9168 (p90) cc_final: 0.8741 (p90) REVERT: B 368 LEU cc_start: 0.9756 (tp) cc_final: 0.9439 (tp) REVERT: B 421 PHE cc_start: 0.9670 (m-80) cc_final: 0.9399 (m-80) REVERT: C 89 TRP cc_start: 0.7923 (m100) cc_final: 0.7669 (m100) REVERT: C 125 HIS cc_start: 0.9626 (m90) cc_final: 0.9408 (m90) REVERT: C 142 TRP cc_start: 0.8983 (p-90) cc_final: 0.8739 (p-90) REVERT: C 188 TYR cc_start: 0.9358 (t80) cc_final: 0.8826 (t80) REVERT: C 201 PHE cc_start: 0.9397 (t80) cc_final: 0.9093 (t80) REVERT: C 236 GLN cc_start: 0.8786 (pt0) cc_final: 0.8579 (pt0) REVERT: C 285 ASP cc_start: 0.9682 (p0) cc_final: 0.9283 (t0) REVERT: C 371 CYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8735 (t) REVERT: C 426 LEU cc_start: 0.9488 (tp) cc_final: 0.9237 (pp) REVERT: D 10 LYS cc_start: 0.9729 (mppt) cc_final: 0.9507 (mmtm) REVERT: D 29 LEU cc_start: 0.9812 (mt) cc_final: 0.9539 (pp) REVERT: D 88 MET cc_start: 0.9373 (pmm) cc_final: 0.8878 (pmm) REVERT: D 97 ASP cc_start: 0.9602 (m-30) cc_final: 0.9339 (m-30) REVERT: D 117 ASP cc_start: 0.9706 (t0) cc_final: 0.9393 (t0) REVERT: D 188 TYR cc_start: 0.9554 (t80) cc_final: 0.9220 (t80) REVERT: D 201 PHE cc_start: 0.9479 (t80) cc_final: 0.9187 (t80) REVERT: D 242 GLU cc_start: 0.9770 (mp0) cc_final: 0.9466 (pm20) REVERT: D 343 ASN cc_start: 0.9691 (p0) cc_final: 0.9424 (m-40) REVERT: D 353 PHE cc_start: 0.9709 (t80) cc_final: 0.9454 (t80) REVERT: D 391 TYR cc_start: 0.8844 (t80) cc_final: 0.8413 (t80) REVERT: D 434 LEU cc_start: 0.9504 (tp) cc_final: 0.9255 (pp) REVERT: P 118 LEU cc_start: 0.9910 (tp) cc_final: 0.9658 (tt) REVERT: P 125 TYR cc_start: 0.9492 (m-10) cc_final: 0.9169 (m-80) REVERT: P 154 LYS cc_start: 0.8323 (tttt) cc_final: 0.8100 (tptt) REVERT: P 155 LYS cc_start: 0.9402 (mmtm) cc_final: 0.9161 (pptt) REVERT: P 159 TYR cc_start: 0.9586 (m-80) cc_final: 0.9308 (m-80) REVERT: P 163 TYR cc_start: 0.9222 (p90) cc_final: 0.8821 (p90) REVERT: Q 127 CYS cc_start: 0.9525 (t) cc_final: 0.9181 (p) REVERT: Q 134 PHE cc_start: 0.9478 (m-80) cc_final: 0.8970 (m-80) REVERT: Q 140 GLU cc_start: 0.9581 (pm20) cc_final: 0.9314 (mm-30) REVERT: Q 163 TYR cc_start: 0.9199 (t80) cc_final: 0.8911 (t80) REVERT: Q 165 ASP cc_start: 0.9455 (p0) cc_final: 0.8923 (p0) REVERT: Q 196 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8900 (mp0) REVERT: Q 247 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8808 (pttm) REVERT: R 117 MET cc_start: 0.9651 (pmm) cc_final: 0.9401 (tmm) REVERT: R 134 PHE cc_start: 0.9317 (m-80) cc_final: 0.9103 (m-80) REVERT: R 155 LYS cc_start: 0.9145 (pttt) cc_final: 0.8689 (ttpp) REVERT: R 160 ASP cc_start: 0.9611 (m-30) cc_final: 0.9294 (t0) REVERT: R 199 ARG cc_start: 0.9475 (ptt-90) cc_final: 0.8630 (ttm110) REVERT: R 239 LEU cc_start: 0.9220 (mm) cc_final: 0.8620 (pp) REVERT: R 244 TRP cc_start: 0.9543 (m-90) cc_final: 0.9220 (m-90) REVERT: R 247 LYS cc_start: 0.9737 (mmmm) cc_final: 0.9369 (tptp) REVERT: S 146 GLU cc_start: 0.9565 (pp20) cc_final: 0.9287 (pp20) REVERT: S 155 LYS cc_start: 0.9601 (ptpp) cc_final: 0.9316 (pptt) REVERT: S 158 ILE cc_start: 0.9690 (tp) cc_final: 0.9313 (pt) REVERT: S 170 MET cc_start: 0.9638 (mmp) cc_final: 0.9406 (mmp) REVERT: S 253 ASP cc_start: 0.9416 (t0) cc_final: 0.8931 (t0) REVERT: a 34 GLU cc_start: 0.8722 (pt0) cc_final: 0.8431 (pm20) REVERT: a 35 GLU cc_start: 0.9337 (tp30) cc_final: 0.9079 (tm-30) REVERT: a 52 MET cc_start: 0.9428 (mtm) cc_final: 0.8841 (mtp) REVERT: a 53 PHE cc_start: 0.9758 (m-80) cc_final: 0.9050 (m-80) REVERT: a 65 MET cc_start: 0.9600 (tmm) cc_final: 0.9397 (ppp) REVERT: a 127 LYS cc_start: 0.9576 (tmtt) cc_final: 0.9191 (tmtt) REVERT: a 267 LEU cc_start: 0.9776 (tp) cc_final: 0.9550 (mm) REVERT: a 316 PHE cc_start: 0.9488 (m-80) cc_final: 0.9112 (m-80) REVERT: a 391 ASN cc_start: 0.9538 (t0) cc_final: 0.9206 (m-40) REVERT: a 416 LYS cc_start: 0.9641 (mtpt) cc_final: 0.9340 (tmtt) REVERT: b 22 CYS cc_start: 0.8209 (t) cc_final: 0.8005 (t) REVERT: b 47 ILE cc_start: 0.9728 (mt) cc_final: 0.9523 (tp) REVERT: b 68 MET cc_start: 0.9681 (tpt) cc_final: 0.9352 (tpp) REVERT: b 97 TYR cc_start: 0.9442 (p90) cc_final: 0.8474 (p90) REVERT: b 226 TYR cc_start: 0.9099 (m-10) cc_final: 0.8860 (m-80) REVERT: b 283 HIS cc_start: 0.9662 (m90) cc_final: 0.9408 (m-70) REVERT: b 288 HIS cc_start: 0.9235 (m170) cc_final: 0.8946 (m170) REVERT: b 386 LEU cc_start: 0.9608 (mt) cc_final: 0.9311 (mt) REVERT: c 22 CYS cc_start: 0.8983 (t) cc_final: 0.8753 (t) REVERT: c 52 MET cc_start: 0.8583 (mmm) cc_final: 0.7701 (mmm) REVERT: c 65 MET cc_start: 0.9862 (ptp) cc_final: 0.9420 (tmm) REVERT: c 79 ASP cc_start: 0.9544 (p0) cc_final: 0.9134 (p0) REVERT: c 97 TYR cc_start: 0.9150 (m-80) cc_final: 0.8771 (m-80) REVERT: c 102 GLN cc_start: 0.9411 (pt0) cc_final: 0.9100 (pm20) REVERT: c 137 LYS cc_start: 0.9732 (mttt) cc_final: 0.9499 (mttp) REVERT: c 239 ARG cc_start: 0.9522 (mtt180) cc_final: 0.8941 (mmm-85) REVERT: c 244 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8590 (mm-30) REVERT: c 281 ILE cc_start: 0.9839 (mt) cc_final: 0.9612 (mt) REVERT: d 53 PHE cc_start: 0.9193 (m-80) cc_final: 0.8984 (m-80) REVERT: d 68 MET cc_start: 0.9525 (mmm) cc_final: 0.9323 (mmm) REVERT: d 163 TYR cc_start: 0.9177 (p90) cc_final: 0.8900 (p90) REVERT: d 281 ILE cc_start: 0.9496 (mt) cc_final: 0.9164 (tp) REVERT: d 300 ASP cc_start: 0.9795 (m-30) cc_final: 0.9519 (p0) REVERT: d 302 ASN cc_start: 0.9634 (m-40) cc_final: 0.8958 (m-40) REVERT: d 305 ARG cc_start: 0.9209 (ptm160) cc_final: 0.8898 (ttp-170) REVERT: d 413 CYS cc_start: 0.9786 (t) cc_final: 0.9568 (p) outliers start: 7 outliers final: 2 residues processed: 859 average time/residue: 0.2224 time to fit residues: 293.1620 Evaluate side-chains 605 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 602 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 166 optimal weight: 20.0000 chunk 313 optimal weight: 0.0010 chunk 152 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 65 optimal weight: 40.0000 chunk 360 optimal weight: 30.0000 chunk 3 optimal weight: 0.8980 chunk 268 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 245 optimal weight: 10.0000 overall best weight: 3.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 130 GLN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 189 HIS Q 190 HIS ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 140 HIS ** a 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 HIS b 144 HIS b 167 HIS ** b 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 HIS ** c 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 155 HIS ** d 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.051258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.038269 restraints weight = 227923.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.039939 restraints weight = 136719.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.041154 restraints weight = 96029.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.042059 restraints weight = 73690.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.042723 restraints weight = 60087.693| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32595 Z= 0.153 Angle : 0.731 19.243 44485 Z= 0.372 Chirality : 0.048 0.463 4986 Planarity : 0.005 0.087 5694 Dihedral : 7.226 84.183 4739 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.79 % Favored : 92.04 % Rotamer: Outliers : 0.14 % Allowed : 5.22 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.13), residues: 4043 helix: -0.14 (0.25), residues: 454 sheet: -1.68 (0.15), residues: 979 loop : -1.46 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG d 224 TYR 0.026 0.002 TYR c 226 PHE 0.034 0.002 PHE D 95 TRP 0.046 0.002 TRP D 410 HIS 0.010 0.001 HIS d 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (32527) covalent geometry : angle 0.71082 / 0.37 (44340) SS BOND : bond 0.00421 / 0.29 ( 56) SS BOND : angle 1.15269 / 0.77 ( 112) hydrogen bonds : bond 0.04478 / 2.98 ( 919) hydrogen bonds : angle 8.10803 / 5.57 ( 2238) Misc. bond : bond 0.00720 / 0.38 ( 1) link_BETA1-4 : bond 0.01072 / 0.54 ( 8) link_BETA1-4 : angle 3.76557 / 2.23 ( 24) link_NAG-ASN : bond 0.01654 / 0.86 ( 3) link_NAG-ASN : angle 9.91564 / 5.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 765 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9508 (pm20) cc_final: 0.9058 (tp30) REVERT: A 103 MET cc_start: 0.9468 (ppp) cc_final: 0.8760 (ppp) REVERT: A 105 GLU cc_start: 0.8491 (pm20) cc_final: 0.7939 (pm20) REVERT: A 175 ASP cc_start: 0.9565 (m-30) cc_final: 0.9341 (p0) REVERT: A 213 ASP cc_start: 0.9550 (p0) cc_final: 0.9172 (p0) REVERT: A 214 LEU cc_start: 0.9202 (pp) cc_final: 0.8663 (mp) REVERT: A 215 TYR cc_start: 0.9217 (m-10) cc_final: 0.8884 (m-10) REVERT: A 412 LYS cc_start: 0.9565 (mttt) cc_final: 0.9349 (tmtt) REVERT: B 15 TYR cc_start: 0.9566 (t80) cc_final: 0.9016 (t80) REVERT: B 142 TRP cc_start: 0.9008 (p-90) cc_final: 0.8446 (p-90) REVERT: B 175 ASP cc_start: 0.9525 (m-30) cc_final: 0.9222 (p0) REVERT: B 188 TYR cc_start: 0.9031 (t80) cc_final: 0.8742 (t80) REVERT: B 242 GLU cc_start: 0.9838 (tt0) cc_final: 0.9608 (tm-30) REVERT: B 254 ASP cc_start: 0.9827 (m-30) cc_final: 0.9404 (t0) REVERT: B 356 HIS cc_start: 0.9695 (m-70) cc_final: 0.9438 (m90) REVERT: B 366 PHE cc_start: 0.9054 (p90) cc_final: 0.8631 (p90) REVERT: B 368 LEU cc_start: 0.9743 (tp) cc_final: 0.9454 (tp) REVERT: B 421 PHE cc_start: 0.9668 (m-80) cc_final: 0.9410 (m-80) REVERT: C 52 LYS cc_start: 0.9592 (ptpt) cc_final: 0.9354 (pttt) REVERT: C 125 HIS cc_start: 0.9643 (m90) cc_final: 0.9412 (m90) REVERT: C 188 TYR cc_start: 0.9307 (t80) cc_final: 0.8788 (t80) REVERT: C 201 PHE cc_start: 0.9386 (t80) cc_final: 0.9059 (t80) REVERT: C 285 ASP cc_start: 0.9717 (p0) cc_final: 0.9325 (t0) REVERT: C 426 LEU cc_start: 0.9450 (tp) cc_final: 0.9232 (pp) REVERT: D 29 LEU cc_start: 0.9803 (mt) cc_final: 0.9601 (pp) REVERT: D 105 GLU cc_start: 0.9204 (pt0) cc_final: 0.8886 (pm20) REVERT: D 188 TYR cc_start: 0.9520 (t80) cc_final: 0.9189 (t80) REVERT: D 343 ASN cc_start: 0.9704 (p0) cc_final: 0.9370 (m-40) REVERT: D 353 PHE cc_start: 0.9774 (t80) cc_final: 0.9560 (t80) REVERT: D 391 TYR cc_start: 0.8929 (t80) cc_final: 0.8289 (t80) REVERT: D 427 ILE cc_start: 0.9370 (pt) cc_final: 0.9134 (pt) REVERT: D 434 LEU cc_start: 0.9501 (tp) cc_final: 0.9252 (pp) REVERT: P 125 TYR cc_start: 0.9519 (m-10) cc_final: 0.9244 (m-80) REVERT: P 163 TYR cc_start: 0.9289 (p90) cc_final: 0.8880 (p90) REVERT: P 242 VAL cc_start: 0.9741 (p) cc_final: 0.9430 (t) REVERT: Q 127 CYS cc_start: 0.9630 (t) cc_final: 0.9352 (m) REVERT: Q 134 PHE cc_start: 0.9458 (m-80) cc_final: 0.9153 (m-80) REVERT: Q 135 LYS cc_start: 0.9346 (pptt) cc_final: 0.9132 (pptt) REVERT: Q 140 GLU cc_start: 0.9645 (pm20) cc_final: 0.9275 (mp0) REVERT: Q 152 LYS cc_start: 0.9627 (tmtt) cc_final: 0.9363 (tptp) REVERT: Q 159 TYR cc_start: 0.9390 (m-80) cc_final: 0.9052 (m-80) REVERT: Q 163 TYR cc_start: 0.9221 (t80) cc_final: 0.8911 (t80) REVERT: Q 165 ASP cc_start: 0.9458 (p0) cc_final: 0.8823 (p0) REVERT: Q 196 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8966 (mp0) REVERT: Q 199 ARG cc_start: 0.9636 (ptp90) cc_final: 0.8980 (ptp-110) REVERT: Q 200 PHE cc_start: 0.9024 (m-10) cc_final: 0.8740 (m-80) REVERT: Q 246 GLN cc_start: 0.9462 (pm20) cc_final: 0.9202 (pm20) REVERT: R 134 PHE cc_start: 0.9400 (m-80) cc_final: 0.9193 (m-80) REVERT: R 153 LEU cc_start: 0.9539 (mp) cc_final: 0.9332 (mp) REVERT: R 155 LYS cc_start: 0.9096 (pttt) cc_final: 0.8664 (ttpp) REVERT: R 160 ASP cc_start: 0.9631 (m-30) cc_final: 0.9260 (t0) REVERT: R 163 TYR cc_start: 0.9556 (p90) cc_final: 0.9135 (p90) REVERT: R 199 ARG cc_start: 0.9463 (ptt-90) cc_final: 0.8935 (ttm110) REVERT: R 239 LEU cc_start: 0.9163 (mm) cc_final: 0.8418 (mt) REVERT: R 247 LYS cc_start: 0.9705 (mmmm) cc_final: 0.9312 (tptp) REVERT: S 125 TYR cc_start: 0.9305 (m-80) cc_final: 0.8828 (m-80) REVERT: S 198 ASN cc_start: 0.9598 (m110) cc_final: 0.9186 (p0) REVERT: S 253 ASP cc_start: 0.9130 (t0) cc_final: 0.8394 (t70) REVERT: a 10 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7967 (mttt) REVERT: a 35 GLU cc_start: 0.9408 (tp30) cc_final: 0.9050 (tm-30) REVERT: a 52 MET cc_start: 0.9395 (mtm) cc_final: 0.9033 (mtp) REVERT: a 53 PHE cc_start: 0.9730 (m-80) cc_final: 0.9193 (m-80) REVERT: a 98 TYR cc_start: 0.8999 (m-10) cc_final: 0.8460 (m-10) REVERT: a 267 LEU cc_start: 0.9781 (tp) cc_final: 0.9529 (mm) REVERT: a 316 PHE cc_start: 0.9392 (m-80) cc_final: 0.9028 (m-80) REVERT: a 342 GLU cc_start: 0.8858 (mp0) cc_final: 0.8570 (mp0) REVERT: a 391 ASN cc_start: 0.9532 (t0) cc_final: 0.9261 (m-40) REVERT: a 416 LYS cc_start: 0.9631 (mtpt) cc_final: 0.9334 (tmtt) REVERT: b 47 ILE cc_start: 0.9733 (mt) cc_final: 0.9524 (tp) REVERT: b 97 TYR cc_start: 0.9416 (p90) cc_final: 0.8434 (p90) REVERT: b 166 MET cc_start: 0.9511 (mpp) cc_final: 0.9247 (mpp) REVERT: b 270 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9198 (tm-30) REVERT: b 288 HIS cc_start: 0.9209 (m170) cc_final: 0.8694 (m170) REVERT: b 316 PHE cc_start: 0.9451 (m-10) cc_final: 0.9223 (m-80) REVERT: c 52 MET cc_start: 0.8828 (mmm) cc_final: 0.8360 (mmm) REVERT: c 77 LYS cc_start: 0.9624 (tptt) cc_final: 0.9399 (tppt) REVERT: c 79 ASP cc_start: 0.9449 (p0) cc_final: 0.9243 (p0) REVERT: c 97 TYR cc_start: 0.9135 (m-80) cc_final: 0.8382 (m-80) REVERT: c 98 TYR cc_start: 0.9590 (m-80) cc_final: 0.9375 (m-80) REVERT: c 102 GLN cc_start: 0.9399 (pt0) cc_final: 0.9003 (pm20) REVERT: c 128 VAL cc_start: 0.9653 (m) cc_final: 0.9421 (m) REVERT: c 160 GLN cc_start: 0.9722 (tm-30) cc_final: 0.9516 (tp-100) REVERT: c 162 HIS cc_start: 0.9502 (t-90) cc_final: 0.9272 (t70) REVERT: c 239 ARG cc_start: 0.9328 (mtt180) cc_final: 0.8940 (mmm-85) REVERT: c 270 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9166 (tm-30) REVERT: c 321 GLU cc_start: 0.9436 (tp30) cc_final: 0.9224 (tp30) REVERT: d 68 MET cc_start: 0.9614 (mmm) cc_final: 0.9245 (mmm) REVERT: d 97 TYR cc_start: 0.9574 (m-10) cc_final: 0.9297 (m-80) REVERT: d 98 TYR cc_start: 0.9652 (m-10) cc_final: 0.9439 (m-10) REVERT: d 163 TYR cc_start: 0.9383 (p90) cc_final: 0.8778 (p90) REVERT: d 240 LEU cc_start: 0.9717 (mt) cc_final: 0.9356 (pp) REVERT: d 244 GLU cc_start: 0.9166 (pm20) cc_final: 0.8911 (pm20) REVERT: d 300 ASP cc_start: 0.9788 (m-30) cc_final: 0.9482 (p0) REVERT: d 302 ASN cc_start: 0.9588 (m-40) cc_final: 0.8917 (m-40) REVERT: d 352 VAL cc_start: 0.9550 (m) cc_final: 0.9325 (m) REVERT: d 355 TYR cc_start: 0.8629 (m-80) cc_final: 0.8287 (m-80) outliers start: 5 outliers final: 0 residues processed: 769 average time/residue: 0.2249 time to fit residues: 267.4243 Evaluate side-chains 561 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 561 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 388 optimal weight: 30.0000 chunk 64 optimal weight: 0.6980 chunk 391 optimal weight: 30.0000 chunk 394 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 324 optimal weight: 50.0000 chunk 209 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 219 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 HIS b 346 HIS ** c 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 114 HIS ** d 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.038110 restraints weight = 226586.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.039763 restraints weight = 136925.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.040961 restraints weight = 96522.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.041861 restraints weight = 74356.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.042521 restraints weight = 60774.375| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32595 Z= 0.145 Angle : 0.701 19.382 44485 Z= 0.356 Chirality : 0.048 0.478 4986 Planarity : 0.006 0.084 5694 Dihedral : 6.359 83.973 4739 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.37 % Favored : 92.46 % Rotamer: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.13), residues: 4043 helix: -0.12 (0.25), residues: 449 sheet: -1.64 (0.15), residues: 986 loop : -1.41 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 224 TYR 0.028 0.002 TYR c 226 PHE 0.026 0.002 PHE D 95 TRP 0.041 0.002 TRP D 410 HIS 0.006 0.001 HIS D 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (32527) covalent geometry : angle 0.68206 / 0.35 (44340) SS BOND : bond 0.00388 / 0.29 ( 56) SS BOND : angle 1.13753 / 0.76 ( 112) hydrogen bonds : bond 0.04013 / 2.69 ( 919) hydrogen bonds : angle 7.65087 / 5.29 ( 2238) Misc. bond : bond 0.00464 / 0.24 ( 1) link_BETA1-4 : bond 0.00959 / 0.49 ( 8) link_BETA1-4 : angle 3.56145 / 2.13 ( 24) link_NAG-ASN : bond 0.01467 / 0.77 ( 3) link_NAG-ASN : angle 9.15636 / 5.13 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 734 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9524 (pm20) cc_final: 0.9075 (tp30) REVERT: A 37 ARG cc_start: 0.9757 (mtp85) cc_final: 0.9240 (ptp90) REVERT: A 81 PHE cc_start: 0.9402 (t80) cc_final: 0.9163 (t80) REVERT: A 103 MET cc_start: 0.9399 (ppp) cc_final: 0.9148 (ppp) REVERT: A 105 GLU cc_start: 0.8351 (pm20) cc_final: 0.7865 (pm20) REVERT: A 175 ASP cc_start: 0.9572 (m-30) cc_final: 0.9313 (p0) REVERT: A 188 TYR cc_start: 0.9713 (t80) cc_final: 0.9473 (t80) REVERT: A 213 ASP cc_start: 0.9483 (p0) cc_final: 0.9155 (p0) REVERT: B 15 TYR cc_start: 0.9560 (t80) cc_final: 0.9096 (t80) REVERT: B 88 MET cc_start: 0.9693 (ppp) cc_final: 0.9367 (ppp) REVERT: B 103 MET cc_start: 0.9093 (tpp) cc_final: 0.8487 (tpp) REVERT: B 142 TRP cc_start: 0.9051 (p-90) cc_final: 0.8414 (p-90) REVERT: B 175 ASP cc_start: 0.9496 (m-30) cc_final: 0.9194 (p0) REVERT: B 188 TYR cc_start: 0.9032 (t80) cc_final: 0.8770 (t80) REVERT: B 242 GLU cc_start: 0.9828 (tt0) cc_final: 0.9610 (tm-30) REVERT: B 254 ASP cc_start: 0.9832 (m-30) cc_final: 0.9419 (t0) REVERT: B 356 HIS cc_start: 0.9685 (m-70) cc_final: 0.9427 (m90) REVERT: B 366 PHE cc_start: 0.9011 (p90) cc_final: 0.8554 (p90) REVERT: B 368 LEU cc_start: 0.9767 (tp) cc_final: 0.9507 (tp) REVERT: B 421 PHE cc_start: 0.9660 (m-80) cc_final: 0.9422 (m-80) REVERT: C 52 LYS cc_start: 0.9600 (ptpt) cc_final: 0.9388 (pttt) REVERT: C 67 GLN cc_start: 0.9491 (pp30) cc_final: 0.9283 (pp30) REVERT: C 125 HIS cc_start: 0.9646 (m90) cc_final: 0.9418 (m90) REVERT: C 188 TYR cc_start: 0.9321 (t80) cc_final: 0.8872 (t80) REVERT: C 204 LEU cc_start: 0.9561 (tp) cc_final: 0.9235 (tp) REVERT: C 243 ARG cc_start: 0.9151 (mtp-110) cc_final: 0.8905 (ptp-110) REVERT: C 268 ARG cc_start: 0.8909 (ttt180) cc_final: 0.8409 (tmm-80) REVERT: C 270 GLU cc_start: 0.9566 (pt0) cc_final: 0.8882 (pm20) REVERT: C 285 ASP cc_start: 0.9718 (p0) cc_final: 0.9318 (t0) REVERT: C 426 LEU cc_start: 0.9455 (tp) cc_final: 0.9219 (pp) REVERT: C 427 ILE cc_start: 0.9660 (pt) cc_final: 0.9440 (pt) REVERT: D 67 GLN cc_start: 0.9013 (pp30) cc_final: 0.8735 (pp30) REVERT: D 142 TRP cc_start: 0.9213 (p-90) cc_final: 0.8904 (p-90) REVERT: D 188 TYR cc_start: 0.9625 (t80) cc_final: 0.9219 (t80) REVERT: D 243 ARG cc_start: 0.9629 (ptt90) cc_final: 0.9373 (ptt180) REVERT: D 246 ARG cc_start: 0.9849 (mtp85) cc_final: 0.9648 (ttp-170) REVERT: D 247 ASP cc_start: 0.9705 (p0) cc_final: 0.9355 (p0) REVERT: D 299 ASP cc_start: 0.9856 (t0) cc_final: 0.9576 (t0) REVERT: D 322 LYS cc_start: 0.9806 (mmpt) cc_final: 0.9597 (mptt) REVERT: D 343 ASN cc_start: 0.9695 (p0) cc_final: 0.9375 (m-40) REVERT: D 353 PHE cc_start: 0.9764 (t80) cc_final: 0.9546 (t80) REVERT: P 117 MET cc_start: 0.9793 (pmm) cc_final: 0.9523 (pmm) REVERT: P 125 TYR cc_start: 0.9519 (m-10) cc_final: 0.9218 (m-80) REVERT: P 154 LYS cc_start: 0.8411 (tttt) cc_final: 0.8178 (tptt) REVERT: P 163 TYR cc_start: 0.9284 (p90) cc_final: 0.8498 (p90) REVERT: Q 127 CYS cc_start: 0.9627 (t) cc_final: 0.9362 (m) REVERT: Q 134 PHE cc_start: 0.9412 (m-80) cc_final: 0.9118 (m-80) REVERT: Q 135 LYS cc_start: 0.9246 (pptt) cc_final: 0.8878 (pptt) REVERT: Q 140 GLU cc_start: 0.9666 (pm20) cc_final: 0.9358 (mp0) REVERT: Q 152 LYS cc_start: 0.9595 (tmtt) cc_final: 0.9318 (tptp) REVERT: Q 163 TYR cc_start: 0.9223 (t80) cc_final: 0.8888 (t80) REVERT: Q 165 ASP cc_start: 0.9486 (p0) cc_final: 0.8818 (p0) REVERT: Q 196 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8968 (mp0) REVERT: R 155 LYS cc_start: 0.9201 (pttt) cc_final: 0.8727 (ttpp) REVERT: R 160 ASP cc_start: 0.9588 (m-30) cc_final: 0.9229 (t0) REVERT: R 199 ARG cc_start: 0.9457 (ptt-90) cc_final: 0.8899 (ttm110) REVERT: R 239 LEU cc_start: 0.9246 (mm) cc_final: 0.8537 (mt) REVERT: R 247 LYS cc_start: 0.9719 (mmmm) cc_final: 0.9302 (tptp) REVERT: S 125 TYR cc_start: 0.9367 (m-80) cc_final: 0.8824 (m-80) REVERT: S 163 TYR cc_start: 0.9481 (t80) cc_final: 0.9256 (t80) REVERT: S 198 ASN cc_start: 0.9571 (m110) cc_final: 0.9124 (p0) REVERT: S 209 LYS cc_start: 0.9896 (tmtt) cc_final: 0.9643 (mmmt) REVERT: S 253 ASP cc_start: 0.9058 (t0) cc_final: 0.8365 (t0) REVERT: a 10 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7892 (mttt) REVERT: a 13 ARG cc_start: 0.9558 (tmm160) cc_final: 0.9112 (tmt170) REVERT: a 35 GLU cc_start: 0.9574 (tp30) cc_final: 0.9046 (tm-30) REVERT: a 52 MET cc_start: 0.9383 (mtm) cc_final: 0.8973 (mtp) REVERT: a 53 PHE cc_start: 0.9719 (m-80) cc_final: 0.9164 (m-80) REVERT: a 98 TYR cc_start: 0.8986 (m-10) cc_final: 0.8446 (m-10) REVERT: a 127 LYS cc_start: 0.9321 (tptp) cc_final: 0.9085 (tptt) REVERT: a 166 MET cc_start: 0.9686 (ptp) cc_final: 0.9359 (mpp) REVERT: a 240 LEU cc_start: 0.9487 (mm) cc_final: 0.9146 (mm) REVERT: a 267 LEU cc_start: 0.9785 (tp) cc_final: 0.9521 (mm) REVERT: a 316 PHE cc_start: 0.9431 (m-80) cc_final: 0.9051 (m-80) REVERT: a 324 GLU cc_start: 0.8902 (tt0) cc_final: 0.8615 (tt0) REVERT: a 342 GLU cc_start: 0.8729 (mp0) cc_final: 0.8410 (mp0) REVERT: a 391 ASN cc_start: 0.9552 (t0) cc_final: 0.9212 (m-40) REVERT: a 416 LYS cc_start: 0.9634 (mtpt) cc_final: 0.9330 (tmtt) REVERT: b 47 ILE cc_start: 0.9750 (mt) cc_final: 0.9508 (tp) REVERT: b 68 MET cc_start: 0.9693 (tpt) cc_final: 0.9333 (tpp) REVERT: b 97 TYR cc_start: 0.9455 (p90) cc_final: 0.8519 (p90) REVERT: b 166 MET cc_start: 0.9497 (mpp) cc_final: 0.9197 (mpp) REVERT: b 267 LEU cc_start: 0.9602 (mt) cc_final: 0.9292 (mt) REVERT: b 270 GLU cc_start: 0.9476 (mt-10) cc_final: 0.9173 (tm-30) REVERT: b 288 HIS cc_start: 0.9179 (m170) cc_final: 0.8743 (p90) REVERT: b 316 PHE cc_start: 0.9476 (m-80) cc_final: 0.9099 (m-80) REVERT: c 52 MET cc_start: 0.8897 (mmm) cc_final: 0.8452 (mmm) REVERT: c 79 ASP cc_start: 0.9403 (p0) cc_final: 0.9197 (p0) REVERT: c 97 TYR cc_start: 0.9046 (m-80) cc_final: 0.8235 (m-80) REVERT: c 98 TYR cc_start: 0.9624 (m-80) cc_final: 0.9387 (m-80) REVERT: c 102 GLN cc_start: 0.9431 (pt0) cc_final: 0.9012 (pm20) REVERT: c 162 HIS cc_start: 0.9492 (t-90) cc_final: 0.9272 (t70) REVERT: c 239 ARG cc_start: 0.9333 (mtt180) cc_final: 0.8922 (mmm-85) REVERT: d 37 ARG cc_start: 0.9054 (tpm170) cc_final: 0.8714 (tpp-160) REVERT: d 44 VAL cc_start: 0.9649 (m) cc_final: 0.9430 (p) REVERT: d 52 MET cc_start: 0.9562 (ptp) cc_final: 0.9033 (ptp) REVERT: d 53 PHE cc_start: 0.9712 (m-80) cc_final: 0.9338 (m-80) REVERT: d 65 MET cc_start: 0.9572 (tmm) cc_final: 0.9253 (ppp) REVERT: d 97 TYR cc_start: 0.9626 (m-10) cc_final: 0.9401 (m-10) REVERT: d 98 TYR cc_start: 0.9704 (m-10) cc_final: 0.9394 (m-10) REVERT: d 163 TYR cc_start: 0.9373 (p90) cc_final: 0.8714 (p90) REVERT: d 302 ASN cc_start: 0.9563 (m-40) cc_final: 0.9332 (p0) REVERT: d 352 VAL cc_start: 0.9527 (m) cc_final: 0.9290 (m) REVERT: d 399 LEU cc_start: 0.9602 (mm) cc_final: 0.9271 (mm) outliers start: 2 outliers final: 0 residues processed: 735 average time/residue: 0.2146 time to fit residues: 245.1797 Evaluate side-chains 542 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 187 optimal weight: 9.9990 chunk 364 optimal weight: 30.0000 chunk 121 optimal weight: 9.9990 chunk 355 optimal weight: 4.9990 chunk 390 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 127 optimal weight: 40.0000 chunk 199 optimal weight: 40.0000 chunk 109 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 275 optimal weight: 0.0980 overall best weight: 6.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 ASN Q 176 GLN ** S 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 102 GLN b 120 HIS ** b 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 GLN c 120 HIS ** c 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.048725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.035993 restraints weight = 235691.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.037591 restraints weight = 143205.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.038757 restraints weight = 101279.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.039627 restraints weight = 78164.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040271 restraints weight = 64074.626| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32595 Z= 0.182 Angle : 0.700 19.394 44485 Z= 0.359 Chirality : 0.047 0.510 4986 Planarity : 0.006 0.083 5694 Dihedral : 6.130 84.610 4739 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.91 % Favored : 91.94 % Rotamer: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 4043 helix: -0.19 (0.25), residues: 462 sheet: -1.66 (0.15), residues: 987 loop : -1.47 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 37 TYR 0.026 0.002 TYR a 138 PHE 0.021 0.002 PHE D 95 TRP 0.032 0.002 TRP A 244 HIS 0.016 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (32527) covalent geometry : angle 0.68133 / 0.35 (44340) SS BOND : bond 0.00518 / 0.35 ( 56) SS BOND : angle 1.33444 / 0.84 ( 112) hydrogen bonds : bond 0.04032 / 2.72 ( 919) hydrogen bonds : angle 7.50946 / 5.21 ( 2238) Misc. bond : bond 0.00334 / 0.18 ( 1) link_BETA1-4 : bond 0.00840 / 0.42 ( 8) link_BETA1-4 : angle 3.25523 / 1.97 ( 24) link_NAG-ASN : bond 0.01786 / 0.92 ( 3) link_NAG-ASN : angle 9.04184 / 5.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 703 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9472 (pm20) cc_final: 0.9052 (tp30) REVERT: A 37 ARG cc_start: 0.9732 (mtp85) cc_final: 0.9507 (ttm110) REVERT: A 88 MET cc_start: 0.8898 (tmm) cc_final: 0.8178 (tmm) REVERT: A 103 MET cc_start: 0.9402 (ppp) cc_final: 0.8615 (ppp) REVERT: A 105 GLU cc_start: 0.8152 (pm20) cc_final: 0.7506 (pm20) REVERT: A 175 ASP cc_start: 0.9529 (m-30) cc_final: 0.9220 (p0) REVERT: A 188 TYR cc_start: 0.9717 (t80) cc_final: 0.9455 (t80) REVERT: A 213 ASP cc_start: 0.9395 (p0) cc_final: 0.9042 (p0) REVERT: A 215 TYR cc_start: 0.9257 (m-10) cc_final: 0.9056 (m-10) REVERT: A 309 TYR cc_start: 0.8804 (t80) cc_final: 0.8490 (t80) REVERT: B 15 TYR cc_start: 0.9443 (t80) cc_final: 0.9080 (t80) REVERT: B 37 ARG cc_start: 0.9375 (mtp85) cc_final: 0.9119 (mtp85) REVERT: B 88 MET cc_start: 0.9680 (ppp) cc_final: 0.9355 (ppp) REVERT: B 132 MET cc_start: 0.9276 (mmp) cc_final: 0.8887 (mmp) REVERT: B 142 TRP cc_start: 0.9060 (p-90) cc_final: 0.8387 (p-90) REVERT: B 175 ASP cc_start: 0.9411 (m-30) cc_final: 0.9089 (p0) REVERT: B 183 HIS cc_start: 0.9647 (t-90) cc_final: 0.9444 (t-90) REVERT: B 188 TYR cc_start: 0.9126 (t80) cc_final: 0.8845 (t80) REVERT: B 242 GLU cc_start: 0.9838 (tt0) cc_final: 0.9636 (tm-30) REVERT: B 356 HIS cc_start: 0.9704 (m-70) cc_final: 0.9450 (m90) REVERT: B 366 PHE cc_start: 0.8995 (p90) cc_final: 0.8626 (p90) REVERT: B 421 PHE cc_start: 0.9667 (m-10) cc_final: 0.9421 (m-80) REVERT: C 125 HIS cc_start: 0.9655 (m90) cc_final: 0.9431 (m90) REVERT: C 188 TYR cc_start: 0.9413 (t80) cc_final: 0.8967 (t80) REVERT: C 234 PHE cc_start: 0.9675 (p90) cc_final: 0.9468 (p90) REVERT: C 285 ASP cc_start: 0.9741 (p0) cc_final: 0.9336 (t0) REVERT: C 426 LEU cc_start: 0.9456 (tp) cc_final: 0.9218 (pp) REVERT: C 427 ILE cc_start: 0.9681 (pt) cc_final: 0.9439 (pt) REVERT: D 7 MET cc_start: 0.9286 (mmp) cc_final: 0.8700 (mmm) REVERT: D 10 LYS cc_start: 0.9661 (mppt) cc_final: 0.9440 (mmtm) REVERT: D 142 TRP cc_start: 0.9284 (p-90) cc_final: 0.8983 (p-90) REVERT: D 188 TYR cc_start: 0.9697 (t80) cc_final: 0.9363 (t80) REVERT: D 234 PHE cc_start: 0.9703 (p90) cc_final: 0.9409 (p90) REVERT: D 243 ARG cc_start: 0.9604 (ptt90) cc_final: 0.9292 (ptt180) REVERT: D 246 ARG cc_start: 0.9851 (mtp85) cc_final: 0.9625 (ttp-170) REVERT: D 247 ASP cc_start: 0.9728 (p0) cc_final: 0.9210 (p0) REVERT: D 299 ASP cc_start: 0.9805 (t0) cc_final: 0.9472 (t0) REVERT: D 322 LYS cc_start: 0.9782 (mmpt) cc_final: 0.9575 (mptt) REVERT: D 343 ASN cc_start: 0.9695 (p0) cc_final: 0.9404 (m-40) REVERT: D 353 PHE cc_start: 0.9734 (t80) cc_final: 0.9519 (t80) REVERT: D 391 TYR cc_start: 0.8761 (t80) cc_final: 0.8040 (t80) REVERT: P 125 TYR cc_start: 0.9563 (m-10) cc_final: 0.9250 (m-80) REVERT: P 154 LYS cc_start: 0.8525 (tttt) cc_final: 0.8251 (tptt) REVERT: P 163 TYR cc_start: 0.9321 (p90) cc_final: 0.8523 (p90) REVERT: P 247 LYS cc_start: 0.9315 (ptpp) cc_final: 0.9021 (pttm) REVERT: Q 134 PHE cc_start: 0.9143 (m-80) cc_final: 0.8943 (m-80) REVERT: Q 135 LYS cc_start: 0.9365 (pptt) cc_final: 0.8992 (pptt) REVERT: Q 140 GLU cc_start: 0.9662 (pm20) cc_final: 0.9370 (mp0) REVERT: Q 152 LYS cc_start: 0.9607 (tmtt) cc_final: 0.9332 (tptp) REVERT: Q 154 LYS cc_start: 0.9823 (pptt) cc_final: 0.9516 (pptt) REVERT: Q 163 TYR cc_start: 0.9244 (t80) cc_final: 0.8872 (t80) REVERT: Q 165 ASP cc_start: 0.9465 (p0) cc_final: 0.8811 (p0) REVERT: Q 196 GLU cc_start: 0.9211 (mt-10) cc_final: 0.9002 (mp0) REVERT: Q 199 ARG cc_start: 0.9599 (ptp90) cc_final: 0.9021 (ptp-110) REVERT: Q 227 VAL cc_start: 0.9290 (t) cc_final: 0.9025 (t) REVERT: R 155 LYS cc_start: 0.9199 (pttt) cc_final: 0.8951 (ttpp) REVERT: R 160 ASP cc_start: 0.9587 (m-30) cc_final: 0.9205 (t0) REVERT: R 199 ARG cc_start: 0.9472 (ptt-90) cc_final: 0.9104 (ttm110) REVERT: R 217 LEU cc_start: 0.9746 (tp) cc_final: 0.9540 (tp) REVERT: R 239 LEU cc_start: 0.9120 (mm) cc_final: 0.8476 (mt) REVERT: R 247 LYS cc_start: 0.9760 (mmmm) cc_final: 0.9343 (tptp) REVERT: S 125 TYR cc_start: 0.9368 (m-80) cc_final: 0.8879 (m-10) REVERT: S 152 LYS cc_start: 0.9700 (tmtt) cc_final: 0.9465 (tptp) REVERT: S 163 TYR cc_start: 0.9463 (t80) cc_final: 0.9254 (t80) REVERT: S 198 ASN cc_start: 0.9584 (m110) cc_final: 0.9171 (p0) REVERT: S 209 LYS cc_start: 0.9885 (tmtt) cc_final: 0.9643 (mmmt) REVERT: S 247 LYS cc_start: 0.9239 (mttt) cc_final: 0.8573 (tptt) REVERT: S 253 ASP cc_start: 0.8938 (t0) cc_final: 0.8207 (t0) REVERT: a 13 ARG cc_start: 0.9546 (tmm160) cc_final: 0.9086 (tmt170) REVERT: a 35 GLU cc_start: 0.9579 (tp30) cc_final: 0.9102 (tm-30) REVERT: a 39 ASP cc_start: 0.8314 (m-30) cc_final: 0.8100 (m-30) REVERT: a 52 MET cc_start: 0.9368 (mtm) cc_final: 0.8985 (mtp) REVERT: a 53 PHE cc_start: 0.9685 (m-80) cc_final: 0.9047 (m-80) REVERT: a 98 TYR cc_start: 0.8973 (m-10) cc_final: 0.8444 (m-10) REVERT: a 152 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.8536 (mtm180) REVERT: a 166 MET cc_start: 0.9658 (ptp) cc_final: 0.9303 (mpp) REVERT: a 240 LEU cc_start: 0.9515 (mm) cc_final: 0.9138 (mm) REVERT: a 267 LEU cc_start: 0.9793 (tp) cc_final: 0.9499 (mm) REVERT: a 316 PHE cc_start: 0.9445 (m-80) cc_final: 0.9091 (m-80) REVERT: a 324 GLU cc_start: 0.8906 (tt0) cc_final: 0.8649 (tt0) REVERT: a 342 GLU cc_start: 0.8861 (mp0) cc_final: 0.8513 (mp0) REVERT: a 391 ASN cc_start: 0.9527 (t0) cc_final: 0.9201 (m-40) REVERT: b 48 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8722 (tm-30) REVERT: b 68 MET cc_start: 0.9711 (tpt) cc_final: 0.9368 (tpp) REVERT: b 97 TYR cc_start: 0.9475 (p90) cc_final: 0.8671 (p90) REVERT: b 120 HIS cc_start: 0.9492 (m-70) cc_final: 0.9261 (m90) REVERT: b 135 ARG cc_start: 0.9336 (mpp80) cc_final: 0.8831 (mtm-85) REVERT: b 166 MET cc_start: 0.9447 (mpp) cc_final: 0.9245 (mpp) REVERT: b 267 LEU cc_start: 0.9550 (mt) cc_final: 0.9242 (mt) REVERT: b 270 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9217 (tm-30) REVERT: b 316 PHE cc_start: 0.9550 (m-80) cc_final: 0.9231 (m-80) REVERT: c 52 MET cc_start: 0.9107 (mmm) cc_final: 0.8563 (mmm) REVERT: c 97 TYR cc_start: 0.9096 (m-80) cc_final: 0.8317 (m-10) REVERT: c 162 HIS cc_start: 0.9545 (t-90) cc_final: 0.9283 (t-90) REVERT: c 166 MET cc_start: 0.9201 (mpp) cc_final: 0.8987 (mpp) REVERT: c 239 ARG cc_start: 0.9294 (mtt180) cc_final: 0.8895 (mmm-85) REVERT: d 39 ASP cc_start: 0.8620 (m-30) cc_final: 0.8011 (p0) REVERT: d 44 VAL cc_start: 0.9654 (m) cc_final: 0.9442 (p) REVERT: d 52 MET cc_start: 0.9608 (ptp) cc_final: 0.8657 (ptp) REVERT: d 53 PHE cc_start: 0.9664 (m-80) cc_final: 0.9424 (m-80) REVERT: d 65 MET cc_start: 0.9586 (tmm) cc_final: 0.9374 (ppp) REVERT: d 68 MET cc_start: 0.9540 (mmp) cc_final: 0.9011 (mmm) REVERT: d 98 TYR cc_start: 0.9698 (m-10) cc_final: 0.9420 (m-10) REVERT: d 99 ILE cc_start: 0.9858 (mm) cc_final: 0.9655 (mm) REVERT: d 140 HIS cc_start: 0.9750 (t-90) cc_final: 0.9548 (t-90) REVERT: d 143 GLU cc_start: 0.9598 (pm20) cc_final: 0.8999 (tm-30) REVERT: d 163 TYR cc_start: 0.9364 (p90) cc_final: 0.8665 (p90) REVERT: d 283 HIS cc_start: 0.9617 (m-70) cc_final: 0.8967 (m-70) REVERT: d 285 HIS cc_start: 0.9143 (p-80) cc_final: 0.8611 (p90) REVERT: d 288 HIS cc_start: 0.9654 (m-70) cc_final: 0.9362 (m-70) REVERT: d 355 TYR cc_start: 0.8531 (m-80) cc_final: 0.8154 (m-80) outliers start: 2 outliers final: 1 residues processed: 704 average time/residue: 0.2010 time to fit residues: 222.3285 Evaluate side-chains 531 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 530 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 66 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 193 optimal weight: 30.0000 chunk 110 optimal weight: 8.9990 chunk 179 optimal weight: 50.0000 chunk 88 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN A 343 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN ** Q 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 138 HIS ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 GLN ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 120 HIS ** c 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.035904 restraints weight = 234393.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.037501 restraints weight = 141630.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.038660 restraints weight = 99903.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.039535 restraints weight = 77302.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040190 restraints weight = 63293.982| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32595 Z= 0.165 Angle : 0.687 19.218 44485 Z= 0.351 Chirality : 0.046 0.326 4986 Planarity : 0.006 0.136 5694 Dihedral : 6.062 87.071 4739 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.09 % Favored : 91.76 % Rotamer: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.13), residues: 4043 helix: -0.04 (0.25), residues: 454 sheet: -1.59 (0.15), residues: 994 loop : -1.47 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG c 152 TYR 0.028 0.002 TYR c 360 PHE 0.028 0.002 PHE A 81 TRP 0.030 0.002 TRP D 410 HIS 0.012 0.001 HIS D 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (32527) covalent geometry : angle 0.67007 / 0.35 (44340) SS BOND : bond 0.00353 / 0.25 ( 56) SS BOND : angle 1.23176 / 0.83 ( 112) hydrogen bonds : bond 0.03893 / 2.63 ( 919) hydrogen bonds : angle 7.32758 / 5.09 ( 2238) Misc. bond : bond 0.00294 / 0.15 ( 1) link_BETA1-4 : bond 0.00931 / 0.47 ( 8) link_BETA1-4 : angle 2.99354 / 1.81 ( 24) link_NAG-ASN : bond 0.01440 / 0.76 ( 3) link_NAG-ASN : angle 8.74792 / 4.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 694 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 20 GLU cc_start: 0.9474 (pm20) cc_final: 0.9068 (tp30) REVERT: A 88 MET cc_start: 0.8810 (tmm) cc_final: 0.8573 (tmm) REVERT: A 103 MET cc_start: 0.9345 (ppp) cc_final: 0.8411 (ttt) REVERT: A 175 ASP cc_start: 0.9546 (m-30) cc_final: 0.9297 (p0) REVERT: A 188 TYR cc_start: 0.9727 (t80) cc_final: 0.9490 (t80) REVERT: A 213 ASP cc_start: 0.9463 (p0) cc_final: 0.8976 (p0) REVERT: A 309 TYR cc_start: 0.8791 (t80) cc_final: 0.8576 (t80) REVERT: B 7 MET cc_start: 0.9602 (tpp) cc_final: 0.9196 (mmm) REVERT: B 15 TYR cc_start: 0.9545 (t80) cc_final: 0.8810 (t80) REVERT: B 37 ARG cc_start: 0.9351 (mtp85) cc_final: 0.9075 (mtp85) REVERT: B 88 MET cc_start: 0.9751 (ppp) cc_final: 0.9368 (ppp) REVERT: B 103 MET cc_start: 0.9009 (tpp) cc_final: 0.8325 (tpp) REVERT: B 132 MET cc_start: 0.9078 (mmp) cc_final: 0.8617 (mmp) REVERT: B 142 TRP cc_start: 0.9040 (p-90) cc_final: 0.8348 (p-90) REVERT: B 175 ASP cc_start: 0.9498 (m-30) cc_final: 0.9203 (p0) REVERT: B 188 TYR cc_start: 0.9030 (t80) cc_final: 0.8776 (t80) REVERT: B 242 GLU cc_start: 0.9835 (tt0) cc_final: 0.9624 (tm-30) REVERT: B 356 HIS cc_start: 0.9705 (m-70) cc_final: 0.9442 (m90) REVERT: B 366 PHE cc_start: 0.8966 (p90) cc_final: 0.8579 (p90) REVERT: C 125 HIS cc_start: 0.9651 (m90) cc_final: 0.9431 (m90) REVERT: C 188 TYR cc_start: 0.9421 (t80) cc_final: 0.9077 (t80) REVERT: C 204 LEU cc_start: 0.9603 (tp) cc_final: 0.9351 (tp) REVERT: C 285 ASP cc_start: 0.9702 (p0) cc_final: 0.9302 (t0) REVERT: C 426 LEU cc_start: 0.9465 (tp) cc_final: 0.9215 (pp) REVERT: D 10 LYS cc_start: 0.9659 (mppt) cc_final: 0.9414 (mmtm) REVERT: D 67 GLN cc_start: 0.8930 (pp30) cc_final: 0.8573 (pp30) REVERT: D 142 TRP cc_start: 0.9292 (p-90) cc_final: 0.8980 (p-90) REVERT: D 188 TYR cc_start: 0.9688 (t80) cc_final: 0.9359 (t80) REVERT: D 234 PHE cc_start: 0.9704 (p90) cc_final: 0.9302 (p90) REVERT: D 246 ARG cc_start: 0.9768 (mtp85) cc_final: 0.9558 (ttm110) REVERT: D 299 ASP cc_start: 0.9805 (t0) cc_final: 0.9483 (t0) REVERT: D 322 LYS cc_start: 0.9779 (mmpt) cc_final: 0.9570 (mptt) REVERT: D 343 ASN cc_start: 0.9614 (p0) cc_final: 0.9318 (m-40) REVERT: D 353 PHE cc_start: 0.9731 (t80) cc_final: 0.9519 (t80) REVERT: D 391 TYR cc_start: 0.8769 (t80) cc_final: 0.8008 (t80) REVERT: P 125 TYR cc_start: 0.9530 (m-10) cc_final: 0.9142 (m-80) REVERT: P 154 LYS cc_start: 0.8580 (tttt) cc_final: 0.8318 (tptt) REVERT: P 163 TYR cc_start: 0.9353 (p90) cc_final: 0.8591 (p90) REVERT: Q 152 LYS cc_start: 0.9600 (tmtt) cc_final: 0.9347 (tptp) REVERT: Q 163 TYR cc_start: 0.9205 (t80) cc_final: 0.8874 (t80) REVERT: Q 165 ASP cc_start: 0.9437 (p0) cc_final: 0.8749 (p0) REVERT: R 138 HIS cc_start: 0.9645 (m-70) cc_final: 0.9402 (m-70) REVERT: R 155 LYS cc_start: 0.9207 (pttt) cc_final: 0.8989 (ttpp) REVERT: R 160 ASP cc_start: 0.9563 (m-30) cc_final: 0.9173 (t0) REVERT: R 199 ARG cc_start: 0.9462 (ptt-90) cc_final: 0.9053 (ttm110) REVERT: R 217 LEU cc_start: 0.9727 (tp) cc_final: 0.9504 (tp) REVERT: R 239 LEU cc_start: 0.9229 (mm) cc_final: 0.8708 (mt) REVERT: R 247 LYS cc_start: 0.9762 (mmmm) cc_final: 0.9330 (tptp) REVERT: S 125 TYR cc_start: 0.9360 (m-80) cc_final: 0.8722 (m-10) REVERT: S 152 LYS cc_start: 0.9650 (tmtt) cc_final: 0.9388 (tptp) REVERT: S 198 ASN cc_start: 0.9578 (m110) cc_final: 0.9166 (p0) REVERT: S 209 LYS cc_start: 0.9904 (tmtt) cc_final: 0.9641 (mmmt) REVERT: S 216 ILE cc_start: 0.9486 (mp) cc_final: 0.9204 (mp) REVERT: S 247 LYS cc_start: 0.9249 (mttt) cc_final: 0.8585 (tptt) REVERT: S 253 ASP cc_start: 0.8793 (t0) cc_final: 0.8038 (t0) REVERT: a 10 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7971 (mttt) REVERT: a 13 ARG cc_start: 0.9526 (tmm160) cc_final: 0.9049 (tmt170) REVERT: a 35 GLU cc_start: 0.9597 (tp30) cc_final: 0.9128 (tm-30) REVERT: a 39 ASP cc_start: 0.8197 (m-30) cc_final: 0.7969 (m-30) REVERT: a 52 MET cc_start: 0.9352 (mtm) cc_final: 0.9006 (mtp) REVERT: a 53 PHE cc_start: 0.9651 (m-80) cc_final: 0.9019 (m-80) REVERT: a 98 TYR cc_start: 0.8963 (m-10) cc_final: 0.8391 (m-10) REVERT: a 152 ARG cc_start: 0.8822 (mtm-85) cc_final: 0.8478 (mtm180) REVERT: a 166 MET cc_start: 0.9638 (ptp) cc_final: 0.9286 (mpp) REVERT: a 267 LEU cc_start: 0.9781 (tp) cc_final: 0.9502 (mm) REVERT: a 276 LYS cc_start: 0.9682 (tmmt) cc_final: 0.9340 (ptpp) REVERT: a 316 PHE cc_start: 0.9462 (m-80) cc_final: 0.9141 (m-80) REVERT: a 324 GLU cc_start: 0.8968 (tt0) cc_final: 0.8647 (tt0) REVERT: a 342 GLU cc_start: 0.8829 (mp0) cc_final: 0.8411 (mp0) REVERT: a 391 ASN cc_start: 0.9516 (t0) cc_final: 0.9192 (m-40) REVERT: a 416 LYS cc_start: 0.9686 (mtpt) cc_final: 0.9420 (tptp) REVERT: b 48 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8803 (tm-30) REVERT: b 68 MET cc_start: 0.9703 (tpt) cc_final: 0.9356 (tpp) REVERT: b 97 TYR cc_start: 0.9465 (p90) cc_final: 0.8654 (p90) REVERT: b 120 HIS cc_start: 0.9510 (m-70) cc_final: 0.9291 (m90) REVERT: b 135 ARG cc_start: 0.9309 (mpp80) cc_final: 0.9036 (mtm180) REVERT: b 205 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8416 (mmt90) REVERT: b 267 LEU cc_start: 0.9545 (mt) cc_final: 0.9228 (mt) REVERT: b 270 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9189 (tm-30) REVERT: b 316 PHE cc_start: 0.9487 (m-80) cc_final: 0.9119 (m-80) REVERT: c 15 TYR cc_start: 0.9254 (t80) cc_final: 0.9045 (t80) REVERT: c 52 MET cc_start: 0.8926 (mmm) cc_final: 0.8547 (mmm) REVERT: c 97 TYR cc_start: 0.8921 (m-80) cc_final: 0.8363 (m-80) REVERT: c 162 HIS cc_start: 0.9550 (t-90) cc_final: 0.9263 (t-90) REVERT: c 166 MET cc_start: 0.8903 (mpp) cc_final: 0.8089 (mpp) REVERT: c 239 ARG cc_start: 0.9189 (mtt180) cc_final: 0.8923 (mmm-85) REVERT: d 44 VAL cc_start: 0.9608 (m) cc_final: 0.9367 (p) REVERT: d 52 MET cc_start: 0.9620 (ptp) cc_final: 0.8650 (ptp) REVERT: d 68 MET cc_start: 0.9529 (mmp) cc_final: 0.9024 (mmm) REVERT: d 98 TYR cc_start: 0.9679 (m-10) cc_final: 0.9171 (m-10) REVERT: d 140 HIS cc_start: 0.9737 (t-90) cc_final: 0.9494 (t-90) REVERT: d 143 GLU cc_start: 0.9592 (pm20) cc_final: 0.8945 (tm-30) REVERT: d 163 TYR cc_start: 0.9353 (p90) cc_final: 0.8657 (p90) REVERT: d 288 HIS cc_start: 0.9656 (m-70) cc_final: 0.9370 (m-70) REVERT: d 355 TYR cc_start: 0.8541 (m-80) cc_final: 0.8156 (m-80) outliers start: 2 outliers final: 0 residues processed: 695 average time/residue: 0.2169 time to fit residues: 236.0897 Evaluate side-chains 517 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 55 optimal weight: 30.0000 chunk 365 optimal weight: 10.0000 chunk 165 optimal weight: 30.0000 chunk 294 optimal weight: 40.0000 chunk 200 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 376 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 149 optimal weight: 30.0000 chunk 258 optimal weight: 20.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 GLN ** P 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 344 ASN ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 GLN c 80 ASN c 82 HIS ** c 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 GLN d 102 GLN ** d 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 391 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.043004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.031740 restraints weight = 261657.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.033152 restraints weight = 157958.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.034171 restraints weight = 111294.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.034937 restraints weight = 85873.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.035504 restraints weight = 70203.370| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 32595 Z= 0.347 Angle : 0.865 19.015 44485 Z= 0.451 Chirality : 0.050 0.561 4986 Planarity : 0.007 0.124 5694 Dihedral : 6.858 85.130 4739 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 37.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.98 % Favored : 88.84 % Rotamer: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 4043 helix: -0.47 (0.23), residues: 467 sheet: -2.10 (0.15), residues: 924 loop : -1.70 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 143 TYR 0.028 0.003 TYR D 391 PHE 0.032 0.003 PHE C 366 TRP 0.038 0.004 TRP A 244 HIS 0.015 0.002 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.35 (32527) covalent geometry : angle 0.84945 / 0.45 (44340) SS BOND : bond 0.00655 / 0.45 ( 56) SS BOND : angle 1.70548 / 1.11 ( 112) hydrogen bonds : bond 0.05275 / 3.53 ( 919) hydrogen bonds : angle 8.06113 / 5.59 ( 2238) Misc. bond : bond 0.00103 / 0.05 ( 1) link_BETA1-4 : bond 0.01057 / 0.53 ( 8) link_BETA1-4 : angle 3.02619 / 1.85 ( 24) link_NAG-ASN : bond 0.01491 / 0.77 ( 3) link_NAG-ASN : angle 8.89955 / 4.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 618 time to evaluate : 1.336 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9494 (pm20) cc_final: 0.9073 (tp30) REVERT: A 88 MET cc_start: 0.9049 (tmm) cc_final: 0.8440 (tmm) REVERT: A 103 MET cc_start: 0.9412 (ppp) cc_final: 0.9120 (ppp) REVERT: A 105 GLU cc_start: 0.8083 (pm20) cc_final: 0.7554 (pm20) REVERT: A 132 MET cc_start: 0.9669 (tpt) cc_final: 0.9379 (tpt) REVERT: A 213 ASP cc_start: 0.9342 (p0) cc_final: 0.9136 (p0) REVERT: A 215 TYR cc_start: 0.9388 (m-10) cc_final: 0.9152 (m-10) REVERT: A 246 ARG cc_start: 0.9705 (ptt180) cc_final: 0.9468 (ptt-90) REVERT: A 309 TYR cc_start: 0.9020 (t80) cc_final: 0.8546 (t80) REVERT: B 15 TYR cc_start: 0.9387 (t80) cc_final: 0.8893 (t80) REVERT: B 88 MET cc_start: 0.9658 (ppp) cc_final: 0.9256 (ppp) REVERT: B 103 MET cc_start: 0.8817 (tpp) cc_final: 0.8272 (tpt) REVERT: B 188 TYR cc_start: 0.9145 (t80) cc_final: 0.8923 (t80) REVERT: B 234 PHE cc_start: 0.9543 (p90) cc_final: 0.9341 (p90) REVERT: B 246 ARG cc_start: 0.9143 (pmt-80) cc_final: 0.8873 (pmt-80) REVERT: B 366 PHE cc_start: 0.8916 (p90) cc_final: 0.8654 (p90) REVERT: C 10 LYS cc_start: 0.9387 (mppt) cc_final: 0.9181 (mmtm) REVERT: C 188 TYR cc_start: 0.9463 (t80) cc_final: 0.9197 (t80) REVERT: C 219 ASN cc_start: 0.9318 (t0) cc_final: 0.8983 (t0) REVERT: C 285 ASP cc_start: 0.9782 (p0) cc_final: 0.9387 (t0) REVERT: D 10 LYS cc_start: 0.9543 (mppt) cc_final: 0.9288 (mmtm) REVERT: D 88 MET cc_start: 0.8965 (pmm) cc_final: 0.8644 (pmm) REVERT: D 142 TRP cc_start: 0.9440 (p-90) cc_final: 0.9178 (p-90) REVERT: D 187 ASN cc_start: 0.9731 (p0) cc_final: 0.9511 (p0) REVERT: D 188 TYR cc_start: 0.9645 (t80) cc_final: 0.9282 (t80) REVERT: D 243 ARG cc_start: 0.9599 (ptt90) cc_final: 0.9310 (ptm-80) REVERT: D 246 ARG cc_start: 0.9814 (mtp85) cc_final: 0.9595 (ttp80) REVERT: D 247 ASP cc_start: 0.9627 (p0) cc_final: 0.9322 (p0) REVERT: D 343 ASN cc_start: 0.9536 (p0) cc_final: 0.9266 (p0) REVERT: D 434 LEU cc_start: 0.9633 (tp) cc_final: 0.9415 (pp) REVERT: P 125 TYR cc_start: 0.9564 (m-80) cc_final: 0.9144 (m-80) REVERT: P 161 LEU cc_start: 0.9349 (tp) cc_final: 0.9068 (tp) REVERT: P 163 TYR cc_start: 0.9462 (p90) cc_final: 0.9015 (p90) REVERT: Q 152 LYS cc_start: 0.9619 (tmtt) cc_final: 0.9374 (tptp) REVERT: Q 163 TYR cc_start: 0.9372 (t80) cc_final: 0.8972 (t80) REVERT: Q 165 ASP cc_start: 0.9400 (p0) cc_final: 0.8643 (p0) REVERT: Q 244 TRP cc_start: 0.9332 (m-90) cc_final: 0.8699 (m-90) REVERT: R 114 PHE cc_start: 0.9649 (m-80) cc_final: 0.9419 (m-80) REVERT: R 119 ASN cc_start: 0.9656 (p0) cc_final: 0.9416 (p0) REVERT: R 138 HIS cc_start: 0.9700 (m-70) cc_final: 0.9437 (m-70) REVERT: R 155 LYS cc_start: 0.9329 (pttt) cc_final: 0.8920 (ptmm) REVERT: R 160 ASP cc_start: 0.9672 (m-30) cc_final: 0.9080 (t0) REVERT: R 170 MET cc_start: 0.9665 (pmm) cc_final: 0.9438 (pmm) REVERT: R 199 ARG cc_start: 0.9549 (ptt-90) cc_final: 0.9326 (ttp80) REVERT: R 217 LEU cc_start: 0.9752 (tp) cc_final: 0.9516 (tp) REVERT: R 247 LYS cc_start: 0.9768 (mmmm) cc_final: 0.9411 (tptp) REVERT: S 125 TYR cc_start: 0.9459 (m-80) cc_final: 0.8660 (m-10) REVERT: S 152 LYS cc_start: 0.9671 (tmtt) cc_final: 0.9404 (tptp) REVERT: S 198 ASN cc_start: 0.9601 (m110) cc_final: 0.9169 (p0) REVERT: S 204 ARG cc_start: 0.9086 (ttm170) cc_final: 0.8850 (mtm180) REVERT: S 209 LYS cc_start: 0.9904 (tmtt) cc_final: 0.9624 (mmmt) REVERT: S 247 LYS cc_start: 0.9389 (mttt) cc_final: 0.9118 (tptt) REVERT: S 253 ASP cc_start: 0.8881 (t0) cc_final: 0.8240 (t0) REVERT: a 10 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8167 (mttt) REVERT: a 13 ARG cc_start: 0.9585 (tmm160) cc_final: 0.9099 (tmt170) REVERT: a 34 GLU cc_start: 0.9026 (pt0) cc_final: 0.8609 (pp20) REVERT: a 35 GLU cc_start: 0.9494 (tp30) cc_final: 0.9006 (tm-30) REVERT: a 39 ASP cc_start: 0.8286 (m-30) cc_final: 0.8022 (m-30) REVERT: a 52 MET cc_start: 0.9378 (mtm) cc_final: 0.8931 (mtm) REVERT: a 53 PHE cc_start: 0.9719 (m-80) cc_final: 0.9101 (m-80) REVERT: a 98 TYR cc_start: 0.8995 (m-10) cc_final: 0.8509 (m-10) REVERT: a 152 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8639 (mtm180) REVERT: a 166 MET cc_start: 0.9635 (ptp) cc_final: 0.9364 (mpp) REVERT: a 240 LEU cc_start: 0.9494 (mm) cc_final: 0.9196 (mm) REVERT: a 280 LEU cc_start: 0.9743 (tp) cc_final: 0.9398 (pp) REVERT: a 316 PHE cc_start: 0.9373 (m-80) cc_final: 0.9049 (m-80) REVERT: a 342 GLU cc_start: 0.9041 (mp0) cc_final: 0.8669 (mp0) REVERT: a 391 ASN cc_start: 0.9546 (t0) cc_final: 0.9217 (m-40) REVERT: a 416 LYS cc_start: 0.9690 (mtpt) cc_final: 0.9391 (tmtt) REVERT: b 48 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8960 (tm-30) REVERT: b 97 TYR cc_start: 0.9505 (p90) cc_final: 0.8776 (p90) REVERT: b 120 HIS cc_start: 0.9507 (m-70) cc_final: 0.9226 (m90) REVERT: b 135 ARG cc_start: 0.9185 (mpp80) cc_final: 0.8722 (mtm180) REVERT: b 267 LEU cc_start: 0.9677 (mt) cc_final: 0.9312 (mt) REVERT: b 310 ARG cc_start: 0.9311 (tpt90) cc_final: 0.8326 (tpt170) REVERT: b 316 PHE cc_start: 0.9554 (m-80) cc_final: 0.9254 (m-80) REVERT: b 386 LEU cc_start: 0.9579 (pp) cc_final: 0.9304 (mt) REVERT: c 52 MET cc_start: 0.8914 (mmm) cc_final: 0.8545 (mmm) REVERT: c 97 TYR cc_start: 0.8925 (m-80) cc_final: 0.8223 (m-80) REVERT: c 162 HIS cc_start: 0.9576 (t-90) cc_final: 0.9324 (t-90) REVERT: c 323 LEU cc_start: 0.9785 (tt) cc_final: 0.9460 (mp) REVERT: d 37 ARG cc_start: 0.9506 (tpm170) cc_final: 0.8963 (tpp-160) REVERT: d 39 ASP cc_start: 0.9005 (m-30) cc_final: 0.8420 (p0) REVERT: d 52 MET cc_start: 0.9442 (ptp) cc_final: 0.8693 (ptp) REVERT: d 68 MET cc_start: 0.9485 (mmp) cc_final: 0.9010 (mmm) REVERT: d 98 TYR cc_start: 0.9659 (m-10) cc_final: 0.9286 (m-10) REVERT: d 140 HIS cc_start: 0.9609 (t-90) cc_final: 0.9313 (t-90) REVERT: d 163 TYR cc_start: 0.9453 (p90) cc_final: 0.8816 (p90) REVERT: d 355 TYR cc_start: 0.8595 (m-80) cc_final: 0.8292 (m-80) REVERT: d 411 LEU cc_start: 0.9607 (mt) cc_final: 0.9407 (mt) outliers start: 2 outliers final: 0 residues processed: 620 average time/residue: 0.2076 time to fit residues: 202.2088 Evaluate side-chains 455 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 189 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 288 optimal weight: 6.9990 chunk 254 optimal weight: 40.0000 chunk 215 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 356 HIS ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 GLN ** Q 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 GLN ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 120 HIS ** c 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 329 ASN ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 391 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.045738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.033346 restraints weight = 229818.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.034896 restraints weight = 136265.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.036045 restraints weight = 95037.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.036896 restraints weight = 72770.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.037532 restraints weight = 59239.565| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32595 Z= 0.162 Angle : 0.725 19.014 44485 Z= 0.371 Chirality : 0.048 0.452 4986 Planarity : 0.006 0.110 5694 Dihedral : 6.449 83.949 4739 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.51 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.13), residues: 4043 helix: -0.19 (0.25), residues: 457 sheet: -1.80 (0.16), residues: 971 loop : -1.54 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 290 TYR 0.022 0.002 TYR c 226 PHE 0.037 0.002 PHE D 95 TRP 0.028 0.002 TRP D 410 HIS 0.007 0.001 HIS a 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (32527) covalent geometry : angle 0.70910 / 0.37 (44340) SS BOND : bond 0.00440 / 0.29 ( 56) SS BOND : angle 1.45022 / 0.94 ( 112) hydrogen bonds : bond 0.03871 / 2.60 ( 919) hydrogen bonds : angle 7.51744 / 5.22 ( 2238) Misc. bond : bond 0.00197 / 0.10 ( 1) link_BETA1-4 : bond 0.00865 / 0.44 ( 8) link_BETA1-4 : angle 2.75737 / 1.67 ( 24) link_NAG-ASN : bond 0.01527 / 0.80 ( 3) link_NAG-ASN : angle 8.71762 / 4.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 20 GLU cc_start: 0.9487 (pm20) cc_final: 0.9115 (tp30) REVERT: A 88 MET cc_start: 0.8884 (tmm) cc_final: 0.8640 (tmm) REVERT: A 103 MET cc_start: 0.9362 (ppp) cc_final: 0.8426 (ttt) REVERT: A 132 MET cc_start: 0.9611 (tpt) cc_final: 0.9373 (tpp) REVERT: A 188 TYR cc_start: 0.9744 (t80) cc_final: 0.9505 (t80) REVERT: A 214 LEU cc_start: 0.8606 (pp) cc_final: 0.8393 (pp) REVERT: A 309 TYR cc_start: 0.8787 (t80) cc_final: 0.8378 (t80) REVERT: A 353 PHE cc_start: 0.9657 (t80) cc_final: 0.9452 (t80) REVERT: B 7 MET cc_start: 0.9652 (tpp) cc_final: 0.9055 (mmm) REVERT: B 15 TYR cc_start: 0.9345 (t80) cc_final: 0.8689 (t80) REVERT: B 37 ARG cc_start: 0.9359 (mtp85) cc_final: 0.9143 (mtp85) REVERT: B 88 MET cc_start: 0.9741 (ppp) cc_final: 0.9399 (ppp) REVERT: B 103 MET cc_start: 0.8937 (tpp) cc_final: 0.8314 (tpp) REVERT: B 132 MET cc_start: 0.8977 (mmp) cc_final: 0.8576 (mmp) REVERT: B 188 TYR cc_start: 0.9104 (t80) cc_final: 0.8778 (t80) REVERT: B 242 GLU cc_start: 0.9741 (tm-30) cc_final: 0.9493 (tm-30) REVERT: B 356 HIS cc_start: 0.9710 (m90) cc_final: 0.9479 (m90) REVERT: B 366 PHE cc_start: 0.8833 (p90) cc_final: 0.8479 (p90) REVERT: C 125 HIS cc_start: 0.9420 (m90) cc_final: 0.9184 (m90) REVERT: C 188 TYR cc_start: 0.9458 (t80) cc_final: 0.9180 (t80) REVERT: C 204 LEU cc_start: 0.9558 (tp) cc_final: 0.9311 (tp) REVERT: C 207 ARG cc_start: 0.9446 (mmt90) cc_final: 0.9123 (mmt90) REVERT: C 219 ASN cc_start: 0.9272 (t0) cc_final: 0.8919 (t0) REVERT: C 285 ASP cc_start: 0.9777 (p0) cc_final: 0.9400 (t0) REVERT: D 10 LYS cc_start: 0.9647 (mppt) cc_final: 0.9379 (mmtm) REVERT: D 88 MET cc_start: 0.8970 (pmm) cc_final: 0.8614 (pmm) REVERT: D 142 TRP cc_start: 0.9392 (p-90) cc_final: 0.9094 (p-90) REVERT: D 188 TYR cc_start: 0.9636 (t80) cc_final: 0.9287 (t80) REVERT: D 234 PHE cc_start: 0.9719 (p90) cc_final: 0.9370 (p90) REVERT: D 343 ASN cc_start: 0.9565 (p0) cc_final: 0.9235 (m-40) REVERT: D 353 PHE cc_start: 0.9743 (t80) cc_final: 0.9500 (t80) REVERT: D 391 TYR cc_start: 0.8894 (t80) cc_final: 0.8096 (t80) REVERT: P 125 TYR cc_start: 0.9542 (m-80) cc_final: 0.9100 (m-80) REVERT: P 163 TYR cc_start: 0.9345 (p90) cc_final: 0.9025 (p90) REVERT: Q 152 LYS cc_start: 0.9606 (tmtt) cc_final: 0.9267 (tptp) REVERT: Q 163 TYR cc_start: 0.9262 (t80) cc_final: 0.8857 (t80) REVERT: Q 165 ASP cc_start: 0.9406 (p0) cc_final: 0.8487 (p0) REVERT: R 114 PHE cc_start: 0.9647 (m-80) cc_final: 0.9350 (m-80) REVERT: R 154 LYS cc_start: 0.9569 (mtmt) cc_final: 0.9337 (mtpt) REVERT: R 155 LYS cc_start: 0.9302 (pttt) cc_final: 0.8931 (ttpp) REVERT: R 160 ASP cc_start: 0.9615 (m-30) cc_final: 0.9210 (t0) REVERT: R 170 MET cc_start: 0.9603 (pmm) cc_final: 0.9367 (pmm) REVERT: R 199 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8591 (mtt180) REVERT: R 217 LEU cc_start: 0.9743 (tp) cc_final: 0.9524 (tp) REVERT: R 247 LYS cc_start: 0.9778 (mmmm) cc_final: 0.9351 (tptp) REVERT: S 125 TYR cc_start: 0.9382 (m-80) cc_final: 0.8656 (m-10) REVERT: S 137 LEU cc_start: 0.9620 (tp) cc_final: 0.9400 (tp) REVERT: S 152 LYS cc_start: 0.9590 (tmtt) cc_final: 0.9305 (tptp) REVERT: S 198 ASN cc_start: 0.9533 (m110) cc_final: 0.9128 (p0) REVERT: S 204 ARG cc_start: 0.9129 (ttm170) cc_final: 0.8847 (mtm180) REVERT: S 209 LYS cc_start: 0.9893 (tmtt) cc_final: 0.9609 (mmmt) REVERT: S 216 ILE cc_start: 0.9539 (mp) cc_final: 0.9259 (mp) REVERT: S 222 ARG cc_start: 0.9835 (mtt180) cc_final: 0.9608 (mtm180) REVERT: S 247 LYS cc_start: 0.9398 (mttt) cc_final: 0.8938 (tptt) REVERT: S 253 ASP cc_start: 0.8779 (t0) cc_final: 0.8033 (t0) REVERT: a 6 PHE cc_start: 0.8986 (p90) cc_final: 0.8750 (p90) REVERT: a 10 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8134 (mttt) REVERT: a 13 ARG cc_start: 0.9527 (tmm160) cc_final: 0.9276 (ttp80) REVERT: a 35 GLU cc_start: 0.9563 (tp30) cc_final: 0.9094 (tm-30) REVERT: a 53 PHE cc_start: 0.9691 (m-80) cc_final: 0.9087 (m-80) REVERT: a 98 TYR cc_start: 0.8942 (m-10) cc_final: 0.8397 (m-10) REVERT: a 152 ARG cc_start: 0.8902 (mtm-85) cc_final: 0.8622 (mtm180) REVERT: a 166 MET cc_start: 0.9626 (ptp) cc_final: 0.9338 (mpp) REVERT: a 240 LEU cc_start: 0.9469 (mm) cc_final: 0.9182 (mm) REVERT: a 316 PHE cc_start: 0.9529 (m-80) cc_final: 0.9191 (m-80) REVERT: a 342 GLU cc_start: 0.8763 (mp0) cc_final: 0.8487 (mp0) REVERT: a 391 ASN cc_start: 0.9469 (t0) cc_final: 0.9161 (m-40) REVERT: a 416 LYS cc_start: 0.9706 (mtpt) cc_final: 0.9431 (tptp) REVERT: b 21 ASN cc_start: 0.9422 (t0) cc_final: 0.9180 (t0) REVERT: b 48 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8747 (tm-30) REVERT: b 68 MET cc_start: 0.9667 (tpp) cc_final: 0.8889 (tpp) REVERT: b 97 TYR cc_start: 0.9505 (p90) cc_final: 0.8413 (p90) REVERT: b 120 HIS cc_start: 0.9547 (m-70) cc_final: 0.9299 (m90) REVERT: b 226 TYR cc_start: 0.9103 (m-80) cc_final: 0.8687 (m-80) REVERT: b 267 LEU cc_start: 0.9652 (mt) cc_final: 0.9331 (mt) REVERT: b 283 HIS cc_start: 0.9558 (m90) cc_final: 0.9330 (m-70) REVERT: b 316 PHE cc_start: 0.9532 (m-80) cc_final: 0.9244 (m-80) REVERT: b 335 VAL cc_start: 0.9346 (t) cc_final: 0.9121 (t) REVERT: b 386 LEU cc_start: 0.9556 (pp) cc_final: 0.9274 (mt) REVERT: c 8 GLN cc_start: 0.9664 (mp10) cc_final: 0.9384 (mp10) REVERT: c 52 MET cc_start: 0.9073 (mmm) cc_final: 0.8680 (mmm) REVERT: c 97 TYR cc_start: 0.8814 (m-80) cc_final: 0.8144 (m-10) REVERT: c 162 HIS cc_start: 0.9568 (t-90) cc_final: 0.9311 (t-90) REVERT: c 166 MET cc_start: 0.8981 (mpp) cc_final: 0.8243 (mpp) REVERT: c 323 LEU cc_start: 0.9806 (tt) cc_final: 0.9556 (mp) REVERT: d 37 ARG cc_start: 0.9426 (tpm170) cc_final: 0.8940 (tpm170) REVERT: d 52 MET cc_start: 0.9417 (ptp) cc_final: 0.8563 (ptp) REVERT: d 65 MET cc_start: 0.9447 (ppp) cc_final: 0.9244 (ppp) REVERT: d 68 MET cc_start: 0.9506 (mmp) cc_final: 0.9093 (mmm) REVERT: d 163 TYR cc_start: 0.9463 (p90) cc_final: 0.8757 (p90) REVERT: d 166 MET cc_start: 0.9473 (ppp) cc_final: 0.9187 (ppp) REVERT: d 355 TYR cc_start: 0.8481 (m-80) cc_final: 0.8169 (m-80) REVERT: d 397 TYR cc_start: 0.6830 (m-10) cc_final: 0.5812 (m-10) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.2114 time to fit residues: 218.7726 Evaluate side-chains 497 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 149 optimal weight: 9.9990 chunk 279 optimal weight: 0.8980 chunk 298 optimal weight: 50.0000 chunk 381 optimal weight: 0.0000 chunk 345 optimal weight: 10.0000 chunk 325 optimal weight: 30.0000 chunk 197 optimal weight: 1.9990 chunk 264 optimal weight: 40.0000 chunk 342 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 overall best weight: 4.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 HIS ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 GLN ** Q 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 GLN ** c 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.046298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.033759 restraints weight = 226543.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.035324 restraints weight = 134603.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.036473 restraints weight = 94084.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.037341 restraints weight = 72107.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.037993 restraints weight = 58722.899| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32595 Z= 0.153 Angle : 0.708 19.198 44485 Z= 0.361 Chirality : 0.047 0.403 4986 Planarity : 0.005 0.095 5694 Dihedral : 6.211 83.721 4739 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.76 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 4043 helix: -0.07 (0.25), residues: 445 sheet: -1.70 (0.16), residues: 930 loop : -1.49 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 152 TYR 0.028 0.002 TYR Q 186 PHE 0.034 0.002 PHE D 95 TRP 0.024 0.002 TRP b 327 HIS 0.015 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (32527) covalent geometry : angle 0.69274 / 0.36 (44340) SS BOND : bond 0.00369 / 0.24 ( 56) SS BOND : angle 1.20345 / 0.78 ( 112) hydrogen bonds : bond 0.03788 / 2.56 ( 919) hydrogen bonds : angle 7.33133 / 5.09 ( 2238) Misc. bond : bond 0.00230 / 0.12 ( 1) link_BETA1-4 : bond 0.00932 / 0.47 ( 8) link_BETA1-4 : angle 2.69967 / 1.65 ( 24) link_NAG-ASN : bond 0.01439 / 0.75 ( 3) link_NAG-ASN : angle 8.65285 / 4.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 20 GLU cc_start: 0.9490 (pm20) cc_final: 0.9118 (tp30) REVERT: A 88 MET cc_start: 0.8805 (tmm) cc_final: 0.8564 (tmm) REVERT: A 103 MET cc_start: 0.9367 (ppp) cc_final: 0.8849 (ttp) REVERT: A 188 TYR cc_start: 0.9731 (t80) cc_final: 0.9424 (t80) REVERT: A 309 TYR cc_start: 0.8782 (t80) cc_final: 0.8509 (t80) REVERT: A 353 PHE cc_start: 0.9667 (t80) cc_final: 0.9459 (t80) REVERT: B 7 MET cc_start: 0.9624 (tpp) cc_final: 0.9055 (mmm) REVERT: B 15 TYR cc_start: 0.9347 (t80) cc_final: 0.8775 (t80) REVERT: B 37 ARG cc_start: 0.9339 (mtp85) cc_final: 0.9023 (mtp85) REVERT: B 88 MET cc_start: 0.9762 (ppp) cc_final: 0.9441 (ppp) REVERT: B 103 MET cc_start: 0.8965 (tpp) cc_final: 0.8399 (tpp) REVERT: B 132 MET cc_start: 0.8978 (mmp) cc_final: 0.8583 (mmp) REVERT: B 175 ASP cc_start: 0.9474 (m-30) cc_final: 0.9219 (p0) REVERT: B 188 TYR cc_start: 0.9127 (t80) cc_final: 0.8882 (t80) REVERT: B 242 GLU cc_start: 0.9755 (tm-30) cc_final: 0.9498 (tm-30) REVERT: B 246 ARG cc_start: 0.8801 (pmt-80) cc_final: 0.8463 (pmt-80) REVERT: B 366 PHE cc_start: 0.8865 (p90) cc_final: 0.8511 (p90) REVERT: C 125 HIS cc_start: 0.9411 (m90) cc_final: 0.9194 (m90) REVERT: C 188 TYR cc_start: 0.9467 (t80) cc_final: 0.9151 (t80) REVERT: C 204 LEU cc_start: 0.9542 (tp) cc_final: 0.9297 (tp) REVERT: C 207 ARG cc_start: 0.9432 (mmt90) cc_final: 0.9108 (mmt90) REVERT: C 219 ASN cc_start: 0.9267 (t0) cc_final: 0.8869 (t0) REVERT: C 285 ASP cc_start: 0.9770 (p0) cc_final: 0.9397 (t0) REVERT: D 10 LYS cc_start: 0.9635 (mppt) cc_final: 0.9364 (mmtm) REVERT: D 67 GLN cc_start: 0.9052 (pp30) cc_final: 0.8730 (pp30) REVERT: D 88 MET cc_start: 0.8996 (pmm) cc_final: 0.8598 (pmm) REVERT: D 142 TRP cc_start: 0.9380 (p-90) cc_final: 0.9063 (p-90) REVERT: D 188 TYR cc_start: 0.9703 (t80) cc_final: 0.9394 (t80) REVERT: D 234 PHE cc_start: 0.9719 (p90) cc_final: 0.9338 (p90) REVERT: D 246 ARG cc_start: 0.9807 (mtp85) cc_final: 0.9564 (ttp80) REVERT: D 247 ASP cc_start: 0.9539 (p0) cc_final: 0.9108 (p0) REVERT: D 343 ASN cc_start: 0.9584 (p0) cc_final: 0.9336 (p0) REVERT: D 353 PHE cc_start: 0.9737 (t80) cc_final: 0.9485 (t80) REVERT: D 391 TYR cc_start: 0.8798 (t80) cc_final: 0.7970 (t80) REVERT: P 125 TYR cc_start: 0.9505 (m-80) cc_final: 0.9073 (m-80) REVERT: Q 152 LYS cc_start: 0.9584 (tmtt) cc_final: 0.9300 (tptp) REVERT: Q 163 TYR cc_start: 0.9216 (t80) cc_final: 0.8778 (t80) REVERT: Q 165 ASP cc_start: 0.9428 (p0) cc_final: 0.8556 (p0) REVERT: Q 186 TYR cc_start: 0.8968 (m-80) cc_final: 0.7928 (m-80) REVERT: R 114 PHE cc_start: 0.9636 (m-80) cc_final: 0.9424 (m-80) REVERT: R 138 HIS cc_start: 0.9633 (m-70) cc_final: 0.9323 (m-70) REVERT: R 154 LYS cc_start: 0.9574 (mtmt) cc_final: 0.9347 (mtpt) REVERT: R 155 LYS cc_start: 0.9298 (pttt) cc_final: 0.8942 (ttpp) REVERT: R 160 ASP cc_start: 0.9554 (m-30) cc_final: 0.9244 (t0) REVERT: R 170 MET cc_start: 0.9540 (pmm) cc_final: 0.9317 (pmm) REVERT: R 247 LYS cc_start: 0.9598 (mmmm) cc_final: 0.9303 (tptp) REVERT: S 106 MET cc_start: 0.9512 (tmm) cc_final: 0.9050 (ptp) REVERT: S 112 LYS cc_start: 0.9688 (mmpt) cc_final: 0.9272 (pttm) REVERT: S 125 TYR cc_start: 0.9351 (m-80) cc_final: 0.8633 (m-10) REVERT: S 137 LEU cc_start: 0.9646 (tp) cc_final: 0.9431 (tp) REVERT: S 152 LYS cc_start: 0.9598 (tmtt) cc_final: 0.9321 (tptp) REVERT: S 154 LYS cc_start: 0.9472 (pptt) cc_final: 0.9266 (pptt) REVERT: S 155 LYS cc_start: 0.9377 (pptt) cc_final: 0.8919 (pptt) REVERT: S 163 TYR cc_start: 0.8746 (t80) cc_final: 0.8514 (t80) REVERT: S 198 ASN cc_start: 0.9515 (m110) cc_final: 0.9180 (p0) REVERT: S 209 LYS cc_start: 0.9893 (tmtt) cc_final: 0.9639 (mmpt) REVERT: S 247 LYS cc_start: 0.9404 (mttt) cc_final: 0.8936 (tptt) REVERT: S 253 ASP cc_start: 0.8750 (t0) cc_final: 0.8003 (t0) REVERT: a 6 PHE cc_start: 0.9001 (p90) cc_final: 0.8741 (p90) REVERT: a 10 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8153 (mttt) REVERT: a 34 GLU cc_start: 0.9126 (pt0) cc_final: 0.8859 (pm20) REVERT: a 35 GLU cc_start: 0.9369 (tp30) cc_final: 0.9159 (tm-30) REVERT: a 53 PHE cc_start: 0.9654 (m-80) cc_final: 0.9158 (m-80) REVERT: a 98 TYR cc_start: 0.8914 (m-10) cc_final: 0.8368 (m-10) REVERT: a 152 ARG cc_start: 0.8895 (mtm-85) cc_final: 0.8607 (mtm180) REVERT: a 166 MET cc_start: 0.9635 (ptp) cc_final: 0.9335 (mpp) REVERT: a 240 LEU cc_start: 0.9415 (mm) cc_final: 0.9079 (mm) REVERT: a 288 HIS cc_start: 0.9741 (m90) cc_final: 0.9453 (m-70) REVERT: a 316 PHE cc_start: 0.9408 (m-80) cc_final: 0.9061 (m-80) REVERT: a 342 GLU cc_start: 0.8723 (mp0) cc_final: 0.8414 (mp0) REVERT: a 391 ASN cc_start: 0.9509 (t0) cc_final: 0.9179 (m-40) REVERT: a 416 LYS cc_start: 0.9702 (mtpt) cc_final: 0.9420 (tptp) REVERT: b 21 ASN cc_start: 0.9436 (t0) cc_final: 0.9184 (t0) REVERT: b 48 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8841 (tm-30) REVERT: b 68 MET cc_start: 0.9644 (tpp) cc_final: 0.9310 (tpp) REVERT: b 97 TYR cc_start: 0.9604 (p90) cc_final: 0.8550 (p90) REVERT: b 120 HIS cc_start: 0.9555 (m-70) cc_final: 0.9319 (m90) REVERT: b 135 ARG cc_start: 0.9172 (mpp80) cc_final: 0.8623 (mtm-85) REVERT: b 226 TYR cc_start: 0.8968 (m-80) cc_final: 0.8685 (m-80) REVERT: b 267 LEU cc_start: 0.9640 (mt) cc_final: 0.9319 (mt) REVERT: b 278 ARG cc_start: 0.8876 (mtm180) cc_final: 0.8653 (mtm180) REVERT: b 283 HIS cc_start: 0.9544 (m90) cc_final: 0.9304 (m-70) REVERT: b 310 ARG cc_start: 0.9199 (tpt90) cc_final: 0.8088 (tpt170) REVERT: b 316 PHE cc_start: 0.9505 (m-80) cc_final: 0.9172 (m-80) REVERT: b 386 LEU cc_start: 0.9491 (pp) cc_final: 0.9248 (mt) REVERT: c 8 GLN cc_start: 0.9612 (mp10) cc_final: 0.9347 (mp10) REVERT: c 52 MET cc_start: 0.9179 (mmm) cc_final: 0.8710 (mmm) REVERT: c 97 TYR cc_start: 0.8841 (m-80) cc_final: 0.8250 (m-80) REVERT: c 162 HIS cc_start: 0.9574 (t-90) cc_final: 0.9251 (t-90) REVERT: c 166 MET cc_start: 0.8998 (mpp) cc_final: 0.8336 (mpp) REVERT: d 52 MET cc_start: 0.9416 (ptp) cc_final: 0.9182 (ptp) REVERT: d 68 MET cc_start: 0.9528 (mmp) cc_final: 0.9176 (mmm) REVERT: d 140 HIS cc_start: 0.9709 (t-90) cc_final: 0.9472 (t-90) REVERT: d 163 TYR cc_start: 0.9499 (p90) cc_final: 0.8911 (p90) REVERT: d 355 TYR cc_start: 0.8490 (m-80) cc_final: 0.8180 (m-80) REVERT: d 397 TYR cc_start: 0.6500 (m-10) cc_final: 0.5291 (m-10) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.2050 time to fit residues: 211.0227 Evaluate side-chains 492 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 362 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 213 optimal weight: 40.0000 chunk 189 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 40 optimal weight: 0.0570 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 HIS ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 GLN ** Q 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 197 ASN ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 GLN c 120 HIS ** c 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.033990 restraints weight = 225995.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.035558 restraints weight = 134192.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.036712 restraints weight = 93847.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.037586 restraints weight = 72022.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.038243 restraints weight = 58583.731| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32595 Z= 0.150 Angle : 0.715 19.585 44485 Z= 0.365 Chirality : 0.048 0.659 4986 Planarity : 0.006 0.103 5694 Dihedral : 6.154 83.717 4739 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.48 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.13), residues: 4043 helix: -0.04 (0.26), residues: 445 sheet: -1.74 (0.16), residues: 955 loop : -1.44 (0.12), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG c 152 TYR 0.026 0.002 TYR c 226 PHE 0.029 0.002 PHE D 95 TRP 0.024 0.002 TRP b 327 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (32527) covalent geometry : angle 0.70052 / 0.36 (44340) SS BOND : bond 0.00326 / 0.22 ( 56) SS BOND : angle 1.28601 / 0.85 ( 112) hydrogen bonds : bond 0.03738 / 2.51 ( 919) hydrogen bonds : angle 7.25269 / 5.05 ( 2238) Misc. bond : bond 0.00207 / 0.11 ( 1) link_BETA1-4 : bond 0.00899 / 0.45 ( 8) link_BETA1-4 : angle 2.66370 / 1.63 ( 24) link_NAG-ASN : bond 0.01212 / 0.64 ( 3) link_NAG-ASN : angle 8.54202 / 4.74 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8086 Ramachandran restraints generated. 4043 Oldfield, 0 Emsley, 4043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 20 GLU cc_start: 0.9514 (pm20) cc_final: 0.9303 (tm-30) REVERT: A 88 MET cc_start: 0.8733 (tmm) cc_final: 0.8461 (tmm) REVERT: A 103 MET cc_start: 0.9351 (ppp) cc_final: 0.8793 (ttt) REVERT: A 188 TYR cc_start: 0.9736 (t80) cc_final: 0.9428 (t80) REVERT: A 215 TYR cc_start: 0.9399 (m-10) cc_final: 0.9143 (m-10) REVERT: A 309 TYR cc_start: 0.8782 (t80) cc_final: 0.8372 (t80) REVERT: A 353 PHE cc_start: 0.9665 (t80) cc_final: 0.9457 (t80) REVERT: A 421 PHE cc_start: 0.9735 (m-80) cc_final: 0.9512 (m-80) REVERT: B 7 MET cc_start: 0.9594 (tpp) cc_final: 0.9072 (mmm) REVERT: B 15 TYR cc_start: 0.9343 (t80) cc_final: 0.8771 (t80) REVERT: B 37 ARG cc_start: 0.9316 (mtp85) cc_final: 0.9042 (mtp85) REVERT: B 88 MET cc_start: 0.9769 (ppp) cc_final: 0.9446 (ppp) REVERT: B 103 MET cc_start: 0.8966 (tpp) cc_final: 0.8407 (tpp) REVERT: B 132 MET cc_start: 0.8973 (mmp) cc_final: 0.8604 (mmp) REVERT: B 175 ASP cc_start: 0.9472 (m-30) cc_final: 0.9229 (p0) REVERT: B 188 TYR cc_start: 0.9148 (t80) cc_final: 0.8885 (t80) REVERT: B 242 GLU cc_start: 0.9729 (tm-30) cc_final: 0.9527 (tm-30) REVERT: B 366 PHE cc_start: 0.8873 (p90) cc_final: 0.8528 (p90) REVERT: C 87 PHE cc_start: 0.9487 (m-80) cc_final: 0.9280 (m-80) REVERT: C 125 HIS cc_start: 0.9416 (m90) cc_final: 0.9200 (m90) REVERT: C 188 TYR cc_start: 0.9460 (t80) cc_final: 0.9175 (t80) REVERT: C 204 LEU cc_start: 0.9541 (tp) cc_final: 0.9313 (tp) REVERT: C 207 ARG cc_start: 0.9430 (mmt90) cc_final: 0.9097 (mmt90) REVERT: C 219 ASN cc_start: 0.9271 (t0) cc_final: 0.8871 (t0) REVERT: C 285 ASP cc_start: 0.9772 (p0) cc_final: 0.9376 (t0) REVERT: D 10 LYS cc_start: 0.9628 (mppt) cc_final: 0.9370 (mmtm) REVERT: D 88 MET cc_start: 0.9023 (pmm) cc_final: 0.8619 (pmm) REVERT: D 142 TRP cc_start: 0.9361 (p-90) cc_final: 0.9031 (p-90) REVERT: D 188 TYR cc_start: 0.9716 (t80) cc_final: 0.9405 (t80) REVERT: D 234 PHE cc_start: 0.9708 (p90) cc_final: 0.9289 (p90) REVERT: D 299 ASP cc_start: 0.9774 (t70) cc_final: 0.9566 (t0) REVERT: D 343 ASN cc_start: 0.9581 (p0) cc_final: 0.9333 (p0) REVERT: D 353 PHE cc_start: 0.9727 (t80) cc_final: 0.9474 (t80) REVERT: D 391 TYR cc_start: 0.8808 (t80) cc_final: 0.8040 (t80) REVERT: P 125 TYR cc_start: 0.9515 (m-80) cc_final: 0.9071 (m-80) REVERT: Q 152 LYS cc_start: 0.9566 (tmtt) cc_final: 0.9251 (tptp) REVERT: Q 163 TYR cc_start: 0.9202 (t80) cc_final: 0.8735 (t80) REVERT: Q 165 ASP cc_start: 0.9399 (p0) cc_final: 0.8431 (p0) REVERT: Q 186 TYR cc_start: 0.9112 (m-80) cc_final: 0.8082 (m-80) REVERT: R 138 HIS cc_start: 0.9623 (m-70) cc_final: 0.9281 (m-70) REVERT: R 154 LYS cc_start: 0.9575 (mtmt) cc_final: 0.9344 (mtpt) REVERT: R 155 LYS cc_start: 0.9304 (pttt) cc_final: 0.8856 (ttpp) REVERT: R 160 ASP cc_start: 0.9559 (m-30) cc_final: 0.9256 (t0) REVERT: R 170 MET cc_start: 0.9496 (pmm) cc_final: 0.9267 (pmm) REVERT: R 247 LYS cc_start: 0.9762 (mmmm) cc_final: 0.9296 (tptp) REVERT: S 106 MET cc_start: 0.9513 (tmm) cc_final: 0.9026 (ptp) REVERT: S 112 LYS cc_start: 0.9688 (mmpt) cc_final: 0.9288 (pttm) REVERT: S 125 TYR cc_start: 0.9368 (m-80) cc_final: 0.8642 (m-10) REVERT: S 137 LEU cc_start: 0.9651 (tp) cc_final: 0.9444 (tp) REVERT: S 146 GLU cc_start: 0.9563 (pp20) cc_final: 0.9362 (pp20) REVERT: S 152 LYS cc_start: 0.9577 (tmtt) cc_final: 0.9296 (tptp) REVERT: S 154 LYS cc_start: 0.9476 (pptt) cc_final: 0.9273 (pptt) REVERT: S 155 LYS cc_start: 0.9388 (pptt) cc_final: 0.8946 (pptt) REVERT: S 163 TYR cc_start: 0.8751 (t80) cc_final: 0.8526 (t80) REVERT: S 198 ASN cc_start: 0.9500 (m110) cc_final: 0.9143 (p0) REVERT: S 209 LYS cc_start: 0.9890 (tmtt) cc_final: 0.9641 (mmmt) REVERT: S 216 ILE cc_start: 0.9579 (mp) cc_final: 0.9329 (mp) REVERT: S 222 ARG cc_start: 0.9830 (mtt180) cc_final: 0.9596 (mtm180) REVERT: S 247 LYS cc_start: 0.9393 (mttt) cc_final: 0.8912 (tptt) REVERT: S 253 ASP cc_start: 0.8639 (t0) cc_final: 0.7864 (t0) REVERT: a 6 PHE cc_start: 0.9006 (p90) cc_final: 0.8714 (p90) REVERT: a 10 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8187 (pttp) REVERT: a 34 GLU cc_start: 0.9149 (pt0) cc_final: 0.8874 (pm20) REVERT: a 35 GLU cc_start: 0.9434 (tp30) cc_final: 0.9186 (tm-30) REVERT: a 39 ASP cc_start: 0.8179 (m-30) cc_final: 0.7649 (m-30) REVERT: a 53 PHE cc_start: 0.9649 (m-80) cc_final: 0.9188 (m-80) REVERT: a 64 TYR cc_start: 0.9827 (m-10) cc_final: 0.9588 (m-80) REVERT: a 98 TYR cc_start: 0.8899 (m-10) cc_final: 0.8347 (m-10) REVERT: a 152 ARG cc_start: 0.8912 (mtm-85) cc_final: 0.8595 (mtm180) REVERT: a 166 MET cc_start: 0.9641 (ptp) cc_final: 0.9367 (mpp) REVERT: a 240 LEU cc_start: 0.9404 (mm) cc_final: 0.9045 (mm) REVERT: a 288 HIS cc_start: 0.9777 (m90) cc_final: 0.9410 (m-70) REVERT: a 316 PHE cc_start: 0.9439 (m-80) cc_final: 0.9149 (m-80) REVERT: a 391 ASN cc_start: 0.9454 (t0) cc_final: 0.9179 (m-40) REVERT: a 416 LYS cc_start: 0.9711 (mtpt) cc_final: 0.9436 (tptp) REVERT: b 21 ASN cc_start: 0.9427 (t0) cc_final: 0.9168 (t0) REVERT: b 48 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8798 (tm-30) REVERT: b 52 MET cc_start: 0.9126 (mpp) cc_final: 0.8816 (mpp) REVERT: b 68 MET cc_start: 0.9532 (tpp) cc_final: 0.9304 (tpp) REVERT: b 97 TYR cc_start: 0.9612 (p90) cc_final: 0.8494 (p90) REVERT: b 120 HIS cc_start: 0.9561 (m-70) cc_final: 0.9314 (m90) REVERT: b 135 ARG cc_start: 0.9087 (mpp80) cc_final: 0.8449 (mtm-85) REVERT: b 226 TYR cc_start: 0.8940 (m-80) cc_final: 0.8675 (m-80) REVERT: b 267 LEU cc_start: 0.9602 (mt) cc_final: 0.9252 (mt) REVERT: b 283 HIS cc_start: 0.9569 (m90) cc_final: 0.9334 (m-70) REVERT: b 316 PHE cc_start: 0.9530 (m-80) cc_final: 0.9174 (m-80) REVERT: b 327 TRP cc_start: 0.8861 (p-90) cc_final: 0.8583 (p-90) REVERT: b 386 LEU cc_start: 0.9519 (pp) cc_final: 0.9235 (mt) REVERT: c 8 GLN cc_start: 0.9582 (mp10) cc_final: 0.9338 (mp10) REVERT: c 52 MET cc_start: 0.9210 (mmm) cc_final: 0.8733 (mmm) REVERT: c 97 TYR cc_start: 0.8714 (m-80) cc_final: 0.8166 (m-80) REVERT: c 162 HIS cc_start: 0.9517 (t-90) cc_final: 0.9240 (t-90) REVERT: c 166 MET cc_start: 0.8964 (mpp) cc_final: 0.8348 (mpp) REVERT: d 52 MET cc_start: 0.9582 (ptp) cc_final: 0.9183 (ptp) REVERT: d 68 MET cc_start: 0.9510 (mmp) cc_final: 0.9204 (mmm) REVERT: d 140 HIS cc_start: 0.9705 (t-90) cc_final: 0.9461 (t-90) REVERT: d 163 TYR cc_start: 0.9523 (p90) cc_final: 0.8918 (p90) REVERT: d 166 MET cc_start: 0.9475 (ppp) cc_final: 0.9154 (ppp) REVERT: d 291 LEU cc_start: 0.9667 (pp) cc_final: 0.9385 (pp) REVERT: d 355 TYR cc_start: 0.8506 (m-80) cc_final: 0.8235 (m-80) REVERT: d 397 TYR cc_start: 0.6323 (m-10) cc_final: 0.5112 (m-10) outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.2001 time to fit residues: 203.2261 Evaluate side-chains 490 residues out of total 3467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 137 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 271 optimal weight: 8.9990 chunk 333 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 HIS ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 GLN ** Q 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 ASN ** a 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 GLN c 120 HIS ** c 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.045844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.033375 restraints weight = 229319.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.034917 restraints weight = 136345.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.036060 restraints weight = 95433.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.036919 restraints weight = 73258.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.037560 restraints weight = 59659.503| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32595 Z= 0.165 Angle : 0.707 19.574 44485 Z= 0.362 Chirality : 0.047 0.490 4986 Planarity : 0.006 0.088 5694 Dihedral : 6.142 83.251 4739 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.93 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.13), residues: 4043 helix: -0.06 (0.25), residues: 445 sheet: -1.77 (0.15), residues: 999 loop : -1.41 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG c 152 TYR 0.026 0.002 TYR c 226 PHE 0.028 0.002 PHE D 95 TRP 0.067 0.002 TRP Q 188 HIS 0.007 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (32527) covalent geometry : angle 0.69217 / 0.36 (44340) SS BOND : bond 0.00327 / 0.22 ( 56) SS BOND : angle 1.27791 / 0.86 ( 112) hydrogen bonds : bond 0.03821 / 2.56 ( 919) hydrogen bonds : angle 7.25045 / 5.05 ( 2238) Misc. bond : bond 0.00234 / 0.12 ( 1) link_BETA1-4 : bond 0.00912 / 0.46 ( 8) link_BETA1-4 : angle 2.64769 / 1.62 ( 24) link_NAG-ASN : bond 0.01277 / 0.67 ( 3) link_NAG-ASN : angle 8.53096 / 4.73 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5837.95 seconds wall clock time: 102 minutes 29.99 seconds (6149.99 seconds total)