Starting phenix.real_space_refine on Tue Aug 26 03:01:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua4_42050/08_2025/8ua4_42050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua4_42050/08_2025/8ua4_42050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ua4_42050/08_2025/8ua4_42050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua4_42050/08_2025/8ua4_42050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ua4_42050/08_2025/8ua4_42050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua4_42050/08_2025/8ua4_42050.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 232 5.16 5 C 21093 2.51 5 N 5753 2.21 5 O 6213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33292 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 411} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3165 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 31, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1110 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 8, 'TRANS': 135} Chain breaks: 8 Chain: "D" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 411} Chain: "E" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3287 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 32, 'TRANS': 385} Chain: "F" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1196 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "G" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 411} Chain: "H" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3258 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 383} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1171 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain breaks: 2 Chain: "J" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3375 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 410} Chain: "K" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3291 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 386} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1187 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 Chain: "M" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "N" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "O" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "P" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 422 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "R" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 274 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} 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: "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 Chain: "E" 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: "G" 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: "H" 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: "J" 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: "K" 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: "M" 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: "N" 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: "O" 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: "P" 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: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.37, per 1000 atoms: 0.25 Number of scatterers: 33292 At special positions: 0 Unit cell: (149.46, 191.86, 190.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 232 16.00 O 6213 8.00 N 5753 7.00 C 21093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=75, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=1.97 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=1.90 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.01 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.00 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=1.93 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.00 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=1.96 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.08 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=1.94 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=2.04 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 217 " distance=2.00 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 413 " distance=2.11 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=1.95 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.05 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.06 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.04 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.13 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=1.97 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.00 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=1.92 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 122 " distance=1.99 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.01 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 103 " distance=1.96 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 263 " distance=1.99 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 223 " distance=1.94 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 217 " distance=2.09 Simple disulfide: pdb=" SG CYS E 393 " - pdb=" SG CYS E 413 " distance=2.18 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=1.94 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=1.95 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.02 Simple disulfide: pdb=" SG CYS G 260 " - pdb=" SG CYS G 272 " distance=2.07 Simple disulfide: pdb=" SG CYS G 302 " - pdb=" SG CYS G 377 " distance=1.96 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 381 " distance=2.04 Simple disulfide: pdb=" SG CYS G 329 " - pdb=" SG CYS G 371 " distance=1.91 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 122 " distance=1.98 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=1.92 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 103 " distance=1.96 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 263 " distance=1.94 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 223 " distance=1.93 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 217 " distance=1.97 Simple disulfide: pdb=" SG CYS H 393 " - pdb=" SG CYS H 413 " distance=2.19 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=1.88 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.06 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.01 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 272 " distance=2.05 Simple disulfide: pdb=" SG CYS J 302 " - pdb=" SG CYS J 377 " distance=2.00 Simple disulfide: pdb=" SG CYS J 307 " - pdb=" SG CYS J 381 " distance=2.05 Simple disulfide: pdb=" SG CYS J 329 " - pdb=" SG CYS J 371 " distance=1.90 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 122 " distance=2.00 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=1.94 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 103 " distance=1.98 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 263 " distance=1.91 Simple disulfide: pdb=" SG CYS K 199 " - pdb=" SG CYS K 223 " distance=1.89 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 217 " distance=2.03 Simple disulfide: pdb=" SG CYS K 393 " - pdb=" SG CYS K 413 " distance=2.13 Simple disulfide: pdb=" SG CYS M 7 " - pdb=" SG CYS M 16 " distance=2.00 Simple disulfide: pdb=" SG CYS M 21 " - pdb=" SG CYS M 25 " distance=2.00 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 56 " distance=2.04 Simple disulfide: pdb=" SG CYS N 7 " - pdb=" SG CYS N 16 " distance=1.92 Simple disulfide: pdb=" SG CYS N 21 " - pdb=" SG CYS N 25 " distance=2.38 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 56 " distance=2.03 Simple disulfide: pdb=" SG CYS O 7 " - pdb=" SG CYS O 16 " distance=2.06 Simple disulfide: pdb=" SG CYS O 21 " - pdb=" SG CYS O 25 " distance=2.23 Simple disulfide: pdb=" SG CYS O 24 " - pdb=" SG CYS O 56 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.01 Simple disulfide: pdb=" SG CYS P 21 " - pdb=" SG CYS P 25 " distance=2.05 Simple disulfide: pdb=" SG CYS P 24 " - pdb=" SG CYS P 56 " distance=2.05 Simple disulfide: pdb=" SG CYS R 33 " - pdb=" SG CYS R 45 " distance=1.99 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 58 " distance=2.01 Simple disulfide: pdb=" SG CYS R 52 " - pdb=" SG CYS R 67 " distance=1.99 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 134 " " NAG B 501 " - " ASN B 315 " " NAG D 501 " - " ASN D 134 " " NAG E 501 " - " ASN E 315 " " NAG G 501 " - " ASN G 134 " " NAG H 501 " - " ASN H 315 " " NAG J 501 " - " ASN J 134 " " NAG K 501 " - " ASN K 315 " " NAG M 101 " - " ASN M 11 " " NAG N 101 " - " ASN N 11 " " NAG O 101 " - " ASN O 11 " " NAG P 101 " - " ASN P 11 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7934 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 95 sheets defined 15.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 225 through 229 removed outlier: 4.021A pdb=" N GLY A 228 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.636A pdb=" N ARG A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 406 through 436 Processing helix chain 'B' and resid 3 through 8 removed outlier: 4.258A pdb=" N GLN B 8 " --> pdb=" O THR B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.505A pdb=" N VAL B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 400 removed outlier: 3.562A pdb=" N THR B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'C' and resid 108 through 111 removed outlier: 3.672A pdb=" N ASP C 111 " --> pdb=" O LEU C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 111' Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.731A pdb=" N ALA C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.717A pdb=" N LYS C 171 " --> pdb=" O GLN C 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 247 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 398 through 402 removed outlier: 4.439A pdb=" N ALA D 402 " --> pdb=" O PHE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 438 Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.988A pdb=" N LYS E 10 " --> pdb=" O THR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 removed outlier: 4.346A pdb=" N GLY E 192 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 360 Processing helix chain 'E' and resid 360 through 400 Proline residue: E 396 - end of helix Processing helix chain 'E' and resid 406 through 413 Processing helix chain 'F' and resid 108 through 111 removed outlier: 3.987A pdb=" N ASP F 111 " --> pdb=" O LEU F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 108 through 111' Processing helix chain 'F' and resid 146 through 151 removed outlier: 4.470A pdb=" N ILE F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 159 No H-bonds generated for 'chain 'F' and resid 157 through 159' Processing helix chain 'F' and resid 167 through 171 removed outlier: 3.676A pdb=" N MET F 170 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 251 through 255 Processing helix chain 'G' and resid 284 through 288 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 398 through 402 removed outlier: 4.599A pdb=" N ALA G 402 " --> pdb=" O PHE G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 438 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 348 through 360 Processing helix chain 'H' and resid 360 through 395 removed outlier: 3.857A pdb=" N THR H 364 " --> pdb=" O TYR H 360 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE H 365 " --> pdb=" O PRO H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 412 removed outlier: 3.903A pdb=" N LEU H 412 " --> pdb=" O LEU H 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'J' and resid 112 through 115 removed outlier: 3.822A pdb=" N SER J 115 " --> pdb=" O GLU J 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 112 through 115' Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'J' and resid 406 through 441 removed outlier: 4.415A pdb=" N HIS J 441 " --> pdb=" O PHE J 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 11 removed outlier: 3.614A pdb=" N LEU K 11 " --> pdb=" O GLN K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 348 through 360 Processing helix chain 'K' and resid 360 through 400 removed outlier: 4.011A pdb=" N ILE K 365 " --> pdb=" O PRO K 361 " (cutoff:3.500A) Proline residue: K 396 - end of helix Processing helix chain 'K' and resid 406 through 413 Processing helix chain 'L' and resid 167 through 171 removed outlier: 3.664A pdb=" N MET L 170 " --> pdb=" O PRO L 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 29 removed outlier: 3.543A pdb=" N LYS M 28 " --> pdb=" O CYS M 24 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN M 29 " --> pdb=" O CYS M 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 24 through 29' Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 45 through 54 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.675A pdb=" N LYS N 28 " --> pdb=" O CYS N 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN N 29 " --> pdb=" O CYS N 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 24 through 29' Processing helix chain 'N' and resid 29 through 34 Processing helix chain 'N' and resid 35 through 40 removed outlier: 3.620A pdb=" N ASN N 40 " --> pdb=" O MET N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 54 removed outlier: 4.145A pdb=" N ALA N 52 " --> pdb=" O GLN N 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 40 removed outlier: 3.852A pdb=" N THR O 35 " --> pdb=" O HIS O 31 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU O 37 " --> pdb=" O THR O 33 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN O 39 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN O 40 " --> pdb=" O MET O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 53 removed outlier: 3.841A pdb=" N LEU O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 29 removed outlier: 4.119A pdb=" N LYS P 28 " --> pdb=" O CYS P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 38 removed outlier: 3.570A pdb=" N THR P 33 " --> pdb=" O ASN P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 54 removed outlier: 3.624A pdb=" N ALA P 52 " --> pdb=" O GLN P 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 51 No H-bonds generated for 'chain 'R' and resid 49 through 51' 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 15 through 19 removed outlier: 5.479A pdb=" N ILE A 31 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU A 33 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASN A 134 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 35 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 132 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 46 removed outlier: 6.942A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 178 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 63 removed outlier: 5.716A pdb=" N THR A 101 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA8, first strand: chain 'A' and resid 297 through 307 removed outlier: 5.432A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 347 removed outlier: 4.132A pdb=" N HIS A 332 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 369 " --> pdb=" O HIS A 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.811A pdb=" N PHE A 366 " --> pdb=" O CYS A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 22 removed outlier: 4.391A pdb=" N ASN B 21 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER B 25 " --> pdb=" O ASN B 21 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 34 through 37 removed outlier: 5.182A pdb=" N GLU B 35 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN B 48 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B 102 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 91 " --> pdb=" O GLN B 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 67 through 68 removed outlier: 3.662A pdb=" N PHE B 67 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 74 " --> pdb=" O PHE B 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.783A pdb=" N THR B 108 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS B 126 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR B 110 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 124 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLY B 112 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N CYS B 122 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 147 through 153 Processing sheet with id=AB8, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB9, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.633A pdb=" N GLY B 207 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.834A pdb=" N LYS B 184 " --> pdb=" O HIS B 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 272 through 276 Processing sheet with id=AC3, first strand: chain 'C' and resid 142 through 143 removed outlier: 4.100A pdb=" N GLY C 124 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 118 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N VAL C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.507A pdb=" N GLN C 176 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA C 225 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N VAL C 224 " --> pdb=" O TRP C 244 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TRP C 244 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER C 240 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY C 230 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA C 238 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 215 through 218 removed outlier: 3.621A pdb=" N ALA C 225 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP C 218 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL C 223 " --> pdb=" O ASP C 218 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC7, first strand: chain 'D' and resid 15 through 19 removed outlier: 5.324A pdb=" N ILE D 31 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU D 33 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN D 134 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN D 35 " --> pdb=" O MET D 132 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TYR D 137 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER D 141 " --> pdb=" O TYR D 137 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 42 through 48 removed outlier: 5.999A pdb=" N LEU D 44 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS D 123 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR D 46 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AD1, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AD2, first strand: chain 'D' and resid 204 through 205 Processing sheet with id=AD3, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AD4, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AD5, first strand: chain 'D' and resid 297 through 307 removed outlier: 4.921A pdb=" N ASP D 299 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 322 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE D 316 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AD7, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AD8, first strand: chain 'E' and resid 17 through 22 removed outlier: 5.671A pdb=" N ASP E 18 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER E 29 " --> pdb=" O ASP E 18 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N CYS E 27 " --> pdb=" O PRO E 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 25 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 34 through 37 removed outlier: 4.696A pdb=" N GLU E 35 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN E 48 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N SER E 50 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N MET E 68 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N TYR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 34 through 37 removed outlier: 4.696A pdb=" N GLU E 35 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN E 48 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TYR E 97 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ALA E 51 " --> pdb=" O HIS E 95 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N HIS E 95 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N PHE E 53 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N SER E 93 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 16.004A pdb=" N LEU E 55 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 18.576A pdb=" N LEU E 91 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 82 through 84 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 153 Processing sheet with id=AE4, first strand: chain 'E' and resid 163 through 164 Processing sheet with id=AE5, first strand: chain 'E' and resid 166 through 167 Processing sheet with id=AE6, first strand: chain 'E' and resid 172 through 173 Processing sheet with id=AE7, first strand: chain 'E' and resid 178 through 181 removed outlier: 3.578A pdb=" N HIS E 213 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 272 through 276 Processing sheet with id=AE9, first strand: chain 'F' and resid 142 through 143 removed outlier: 6.438A pdb=" N PHE F 114 " --> pdb=" O TYR F 125 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR F 125 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 116 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN F 123 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N TYR F 125 " --> pdb=" O PRO F 136 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 250 through 253 removed outlier: 4.986A pdb=" N PHE F 200 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N ALA F 192 " --> pdb=" O PRO F 203 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE F 216 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 250 through 253 removed outlier: 6.826A pdb=" N ARG F 236 " --> pdb=" O ASN F 232 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN F 232 " --> pdb=" O ARG F 236 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA F 238 " --> pdb=" O GLY F 230 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY F 230 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER F 240 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP F 244 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL F 224 " --> pdb=" O TRP F 244 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AF4, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.421A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU G 33 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN G 134 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 15 through 19 Processing sheet with id=AF6, first strand: chain 'G' and resid 184 through 186 removed outlier: 6.623A pdb=" N ALA G 119 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE G 47 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA G 121 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AF8, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF9, first strand: chain 'G' and resid 298 through 307 removed outlier: 4.953A pdb=" N ASP G 299 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS G 322 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE G 316 " --> pdb=" O THR G 305 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE G 353 " --> pdb=" O VAL G 319 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 344 through 347 removed outlier: 3.672A pdb=" N VAL G 345 " --> pdb=" O CYS G 329 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS G 329 " --> pdb=" O VAL G 345 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 327 " --> pdb=" O LEU G 347 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AG3, first strand: chain 'H' and resid 34 through 37 removed outlier: 4.429A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 16.869A pdb=" N GLN H 48 " --> pdb=" O PHE H 67 " (cutoff:3.500A) removed outlier: 13.662A pdb=" N PHE H 67 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 11.828A pdb=" N SER H 50 " --> pdb=" O MET H 65 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N MET H 65 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N MET H 52 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N ALA H 63 " --> pdb=" O MET H 52 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY H 54 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 34 through 37 removed outlier: 4.429A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR H 97 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA H 51 " --> pdb=" O HIS H 95 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N HIS H 95 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE H 53 " --> pdb=" O SER H 93 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N SER H 93 " --> pdb=" O PHE H 53 " (cutoff:3.500A) removed outlier: 16.438A pdb=" N LEU H 55 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 17.913A pdb=" N LEU H 91 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 82 through 84 Processing sheet with id=AG6, first strand: chain 'H' and resid 146 through 153 Processing sheet with id=AG7, first strand: chain 'H' and resid 163 through 164 Processing sheet with id=AG8, first strand: chain 'H' and resid 166 through 167 Processing sheet with id=AG9, first strand: chain 'H' and resid 172 through 174 removed outlier: 4.060A pdb=" N ALA H 225 " --> pdb=" O ASP H 174 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 178 through 181 Processing sheet with id=AH2, first strand: chain 'H' and resid 272 through 276 Processing sheet with id=AH3, first strand: chain 'I' and resid 167 through 171 removed outlier: 8.050A pdb=" N PHE I 167 " --> pdb=" O TYR I 178 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR I 178 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE I 169 " --> pdb=" O ASN I 176 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR I 178 " --> pdb=" O PRO I 189 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 237 through 241 removed outlier: 7.987A pdb=" N ALA I 245 " --> pdb=" O PRO I 256 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE I 253 " --> pdb=" O LEU I 292 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 237 through 241 removed outlier: 7.987A pdb=" N ALA I 245 " --> pdb=" O PRO I 256 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE I 253 " --> pdb=" O LEU I 292 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL I 295 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL I 280 " --> pdb=" O VAL I 295 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.549A pdb=" N LYS J 161 " --> pdb=" O ASP J 282 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE J 164 " --> pdb=" O THR J 153 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR J 153 " --> pdb=" O ILE J 164 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 15 through 19 removed outlier: 5.274A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU J 33 " --> pdb=" O ASN J 134 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASN J 134 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN J 35 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 15 through 19 Processing sheet with id=AH9, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.125A pdb=" N LEU J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS J 123 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AI2, first strand: chain 'J' and resid 87 through 88 removed outlier: 3.705A pdb=" N GLY J 91 " --> pdb=" O MET J 88 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 204 through 206 Processing sheet with id=AI4, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AI5, first strand: chain 'J' and resid 297 through 307 removed outlier: 5.220A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE J 316 " --> pdb=" O THR J 305 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 344 through 347 removed outlier: 4.111A pdb=" N VAL J 345 " --> pdb=" O CYS J 329 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS J 329 " --> pdb=" O VAL J 345 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AI8, first strand: chain 'K' and resid 17 through 19 removed outlier: 3.734A pdb=" N ALA K 17 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS K 27 " --> pdb=" O CYS K 19 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 34 through 37 removed outlier: 4.725A pdb=" N VAL K 36 " --> pdb=" O ARG K 46 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG K 46 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 10.210A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TYR K 64 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N LYS K 56 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU K 62 " --> pdb=" O LYS K 56 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 34 through 37 removed outlier: 4.725A pdb=" N VAL K 36 " --> pdb=" O ARG K 46 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG K 46 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR K 97 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ALA K 51 " --> pdb=" O HIS K 95 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N HIS K 95 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N PHE K 53 " --> pdb=" O SER K 93 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N SER K 93 " --> pdb=" O PHE K 53 " (cutoff:3.500A) removed outlier: 15.160A pdb=" N LEU K 55 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 18.385A pdb=" N LEU K 91 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 82 through 84 Processing sheet with id=AJ3, first strand: chain 'K' and resid 147 through 153 Processing sheet with id=AJ4, first strand: chain 'K' and resid 234 through 235 Processing sheet with id=AJ5, first strand: chain 'K' and resid 172 through 173 Processing sheet with id=AJ6, first strand: chain 'K' and resid 178 through 180 Processing sheet with id=AJ7, first strand: chain 'K' and resid 272 through 276 Processing sheet with id=AJ8, first strand: chain 'L' and resid 142 through 143 removed outlier: 3.824A pdb=" N GLY L 124 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU L 118 " --> pdb=" O VAL L 122 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL L 122 " --> pdb=" O LEU L 118 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 250 through 253 removed outlier: 5.177A pdb=" N PHE L 200 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N ALA L 192 " --> pdb=" O PRO L 203 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU L 259 " --> pdb=" O GLY L 230 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 250 through 253 removed outlier: 6.690A pdb=" N ALA L 238 " --> pdb=" O GLY L 230 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY L 230 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER L 240 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE L 226 " --> pdb=" O VAL L 242 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP L 244 " --> pdb=" O VAL L 224 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL L 224 " --> pdb=" O TRP L 244 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU L 259 " --> pdb=" O GLY L 230 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'M' and resid 6 through 8 Processing sheet with id=AK3, first strand: chain 'N' and resid 6 through 9 Processing sheet with id=AK4, first strand: chain 'P' and resid 7 through 8 Processing sheet with id=AK5, first strand: chain 'R' and resid 37 through 39 1194 hydrogen bonds defined for protein. 2994 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: 8.55 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 11562 1.36 - 1.51: 11637 1.51 - 1.66: 10693 1.66 - 1.82: 255 1.82 - 1.97: 30 Bond restraints: 34177 Sorted by residual: bond pdb=" CB CYS O 21 " pdb=" SG CYS O 21 " ideal model delta sigma weight residual 1.808 1.974 -0.166 3.30e-02 9.18e+02 2.54e+01 bond pdb=" CB CYS G 94 " pdb=" SG CYS G 94 " ideal model delta sigma weight residual 1.808 1.660 0.148 3.30e-02 9.18e+02 2.02e+01 bond pdb=" CB GLU G 152 " pdb=" CG GLU G 152 " ideal model delta sigma weight residual 1.520 1.615 -0.095 3.00e-02 1.11e+03 1.01e+01 bond pdb=" CB CYS H 393 " pdb=" SG CYS H 393 " ideal model delta sigma weight residual 1.808 1.910 -0.102 3.30e-02 9.18e+02 9.63e+00 bond pdb=" CB TYR D 321 " pdb=" CG TYR D 321 " ideal model delta sigma weight residual 1.512 1.449 0.063 2.20e-02 2.07e+03 8.26e+00 ... (remaining 34172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.74: 46090 4.74 - 9.48: 459 9.48 - 14.22: 19 14.22 - 18.95: 3 18.95 - 23.69: 1 Bond angle restraints: 46572 Sorted by residual: angle pdb=" CA CYS O 21 " pdb=" CB CYS O 21 " pdb=" SG CYS O 21 " ideal model delta sigma weight residual 114.40 138.09 -23.69 2.30e+00 1.89e-01 1.06e+02 angle pdb=" CA PRO L 215 " pdb=" N PRO L 215 " pdb=" CD PRO L 215 " ideal model delta sigma weight residual 112.00 98.31 13.69 1.40e+00 5.10e-01 9.56e+01 angle pdb=" CA PRO F 167 " pdb=" N PRO F 167 " pdb=" CD PRO F 167 " ideal model delta sigma weight residual 112.00 99.54 12.46 1.40e+00 5.10e-01 7.92e+01 angle pdb=" CA PRO B 361 " pdb=" N PRO B 361 " pdb=" CD PRO B 361 " ideal model delta sigma weight residual 112.00 100.42 11.58 1.40e+00 5.10e-01 6.84e+01 angle pdb=" CA CYS N 21 " pdb=" CB CYS N 21 " pdb=" SG CYS N 21 " ideal model delta sigma weight residual 114.40 133.25 -18.85 2.30e+00 1.89e-01 6.72e+01 ... (remaining 46567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.35: 17526 18.35 - 36.70: 2457 36.70 - 55.06: 582 55.06 - 73.41: 105 73.41 - 91.76: 41 Dihedral angle restraints: 20711 sinusoidal: 8344 harmonic: 12367 Sorted by residual: dihedral pdb=" CA LEU H 411 " pdb=" C LEU H 411 " pdb=" N LEU H 412 " pdb=" CA LEU H 412 " ideal model delta harmonic sigma weight residual -180.00 -104.94 -75.06 0 5.00e+00 4.00e-02 2.25e+02 dihedral pdb=" CA ALA K 400 " pdb=" C ALA K 400 " pdb=" N PRO K 401 " pdb=" CA PRO K 401 " ideal model delta harmonic sigma weight residual 180.00 -108.09 -71.91 0 5.00e+00 4.00e-02 2.07e+02 dihedral pdb=" CA LEU N 9 " pdb=" C LEU N 9 " pdb=" N ALA N 10 " pdb=" CA ALA N 10 " ideal model delta harmonic sigma weight residual 180.00 -120.88 -59.12 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 20708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 5003 0.146 - 0.292: 211 0.292 - 0.437: 13 0.437 - 0.583: 1 0.583 - 0.729: 2 Chirality restraints: 5230 Sorted by residual: chirality pdb=" C1 NAG G 501 " pdb=" ND2 ASN G 134 " pdb=" C2 NAG G 501 " pdb=" O5 NAG G 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 315 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA PHE B 53 " pdb=" N PHE B 53 " pdb=" C PHE B 53 " pdb=" CB PHE B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 5227 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 360 " -0.125 5.00e-02 4.00e+02 1.79e-01 5.12e+01 pdb=" N PRO B 361 " 0.309 5.00e-02 4.00e+02 pdb=" CA PRO B 361 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO B 361 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 254 " -0.117 5.00e-02 4.00e+02 1.70e-01 4.64e+01 pdb=" N PRO F 255 " 0.294 5.00e-02 4.00e+02 pdb=" CA PRO F 255 " -0.094 5.00e-02 4.00e+02 pdb=" CD PRO F 255 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 214 " -0.120 5.00e-02 4.00e+02 1.68e-01 4.51e+01 pdb=" N PRO L 215 " 0.290 5.00e-02 4.00e+02 pdb=" CA PRO L 215 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO L 215 " -0.083 5.00e-02 4.00e+02 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 425 2.57 - 3.15: 28208 3.15 - 3.73: 50698 3.73 - 4.32: 68330 4.32 - 4.90: 116897 Nonbonded interactions: 264558 Sorted by model distance: nonbonded pdb=" OH TYR D 321 " pdb=" O ALA D 348 " model vdw 1.984 3.040 nonbonded pdb=" OG1 THR A 218 " pdb=" OE1 GLN A 236 " model vdw 1.986 3.040 nonbonded pdb=" O ASN K 402 " pdb=" OH TYR L 177 " model vdw 1.996 3.040 nonbonded pdb=" OG SER G 292 " pdb=" OE2 GLU G 293 " model vdw 2.002 3.040 nonbonded pdb=" OE2 GLU A 397 " pdb=" OH TYR B 360 " model vdw 2.011 3.040 ... (remaining 264553 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 'D' and (resid 1 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 501)) selection = (chain 'G' and (resid 1 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 501)) selection = (chain 'J' and (resid 1 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 501)) } ncs_group { reference = (chain 'B' and (resid 2 through 165 or (resid 166 and (name N or name CA or name \ C or name O or name CB )) or resid 167 through 248 or (resid 249 and (name N or \ name CA or name C or name O or name CB )) or resid 250 through 501)) selection = (chain 'E' and (resid 2 through 53 or resid 66 through 165 or (resid 166 and (na \ me N or name CA or name C or name O or name CB )) or resid 167 through 248 or (r \ esid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 t \ hrough 415 or resid 501)) selection = (chain 'H' and (resid 2 through 53 or resid 66 through 248 or (resid 249 and (na \ me N or name CA or name C or name O or name CB )) or resid 250 through 501)) selection = (chain 'K' and (resid 2 through 53 or resid 66 through 165 or (resid 166 and (na \ me N or name CA or name C or name O or name CB )) or resid 167 through 415 or re \ sid 501)) } ncs_group { reference = (chain 'C' and (resid 109 through 218 or resid 221 through 261)) selection = (chain 'F' and (resid 109 through 183 or resid 186 through 191 or resid 193 or r \ esid 195 or resid 197 through 202 or resid 204 through 205 or resid 207 through \ 218 or resid 221 through 234 or resid 237 through 261)) selection = (chain 'I' and (resid 162 through 236 or resid 239 through 244 or resid 246 or r \ esid 248 or resid 250 through 255 or resid 257 through 258 or resid 260 through \ 287 or resid 290 through 314)) selection = (chain 'L' and (resid 109 through 183 or resid 186 through 191 or resid 193 or r \ esid 195 or resid 197 through 202 or resid 204 through 205 or resid 207 through \ 218 or resid 221 through 234 or resid 237 through 261)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.00 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.760 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 0.013 0.350 34264 Z= 0.591 Angle : 1.296 23.692 46758 Z= 0.705 Chirality : 0.072 0.729 5230 Planarity : 0.012 0.179 5982 Dihedral : 17.668 91.760 12552 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 0.57 % Favored : 99.41 % Rotamer: Outliers : 1.31 % Allowed : 32.62 % Favored : 66.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 1.34 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.12), residues: 4220 helix: -1.50 (0.21), residues: 506 sheet: -0.82 (0.15), residues: 1168 loop : -1.89 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 199 TYR 0.051 0.004 TYR B 98 PHE 0.085 0.004 PHE B 53 TRP 0.048 0.003 TRP L 244 HIS 0.060 0.003 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.01256 (34177) covalent geometry : angle 1.27161 (46572) SS BOND : bond 0.08278 ( 75) SS BOND : angle 4.07192 ( 150) hydrogen bonds : bond 0.14532 ( 1152) hydrogen bonds : angle 8.42643 ( 2994) link_NAG-ASN : bond 0.00914 ( 12) link_NAG-ASN : angle 4.67793 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 777 time to evaluate : 1.175 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: F 117 MET cc_start: 0.7015 (mmm) cc_final: 0.6168 (mmm) REVERT: G 100 ASN cc_start: 0.7678 (m-40) cc_final: 0.7259 (m-40) REVERT: L 178 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.5506 (t) REVERT: L 190 HIS cc_start: 0.7058 (m-70) cc_final: 0.6770 (m90) REVERT: L 195 TYR cc_start: 0.6239 (t80) cc_final: 0.6035 (t80) REVERT: M 33 THR cc_start: 0.8709 (m) cc_final: 0.8234 (p) REVERT: P 49 LEU cc_start: 0.7769 (tt) cc_final: 0.6873 (tt) outliers start: 48 outliers final: 14 residues processed: 816 average time/residue: 0.2499 time to fit residues: 313.7490 Evaluate side-chains 497 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 482 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 321 TYR Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain K residue 199 CYS Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain L residue 178 THR Chi-restraints excluded: chain P residue 11 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 212 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 79 GLN G 130 GLN H 102 GLN ** H 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** K 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS L 119 ASN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 232 ASN M 40 ASN M 57 ASN N 48 GLN O 29 ASN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.099750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.089436 restraints weight = 241715.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.089176 restraints weight = 118540.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.089227 restraints weight = 72397.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.089314 restraints weight = 58688.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.089767 restraints weight = 48727.325| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 34264 Z= 0.205 Angle : 0.870 13.386 46758 Z= 0.441 Chirality : 0.051 0.498 5230 Planarity : 0.008 0.115 5982 Dihedral : 7.540 64.173 4880 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.33 % Favored : 93.53 % Rotamer: Outliers : 5.59 % Allowed : 29.24 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.67 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.12), residues: 4220 helix: -0.79 (0.21), residues: 535 sheet: -0.68 (0.15), residues: 1169 loop : -1.66 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 132 TYR 0.024 0.002 TYR B 98 PHE 0.025 0.002 PHE D 399 TRP 0.045 0.002 TRP F 244 HIS 0.013 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00455 (34177) covalent geometry : angle 0.85379 (46572) SS BOND : bond 0.00431 ( 75) SS BOND : angle 2.25762 ( 150) hydrogen bonds : bond 0.04520 ( 1152) hydrogen bonds : angle 6.78917 ( 2994) link_NAG-ASN : bond 0.00762 ( 12) link_NAG-ASN : angle 4.44769 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 511 time to evaluate : 1.429 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: A 241 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8196 (m-10) REVERT: A 349 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: B 212 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.9036 (t0) REVERT: B 233 TRP cc_start: 0.9406 (OUTLIER) cc_final: 0.9129 (m-10) REVERT: B 275 HIS cc_start: 0.9256 (OUTLIER) cc_final: 0.9021 (m-70) REVERT: B 339 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: B 365 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8908 (mp) REVERT: B 386 LEU cc_start: 0.9757 (pp) cc_final: 0.9475 (mm) REVERT: C 125 TYR cc_start: 0.9410 (m-80) cc_final: 0.8529 (t80) REVERT: C 145 ASN cc_start: 0.9550 (t0) cc_final: 0.9115 (t0) REVERT: C 159 TYR cc_start: 0.9441 (m-80) cc_final: 0.8707 (m-80) REVERT: C 200 PHE cc_start: 0.8906 (m-10) cc_final: 0.8655 (m-10) REVERT: C 218 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.7618 (p0) REVERT: C 253 ASP cc_start: 0.8863 (t0) cc_final: 0.8455 (t0) REVERT: D 204 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9334 (mp) REVERT: D 421 PHE cc_start: 0.9753 (m-80) cc_final: 0.9443 (t80) REVERT: D 439 HIS cc_start: 0.8600 (m90) cc_final: 0.7933 (m90) REVERT: E 52 MET cc_start: 0.9162 (mmm) cc_final: 0.8817 (mmm) REVERT: E 247 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7970 (p) REVERT: E 270 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8986 (tp30) REVERT: E 287 ASP cc_start: 0.9179 (p0) cc_final: 0.8798 (p0) REVERT: E 302 ASN cc_start: 0.9604 (t0) cc_final: 0.9347 (t0) REVERT: E 306 GLN cc_start: 0.8343 (pm20) cc_final: 0.8109 (pm20) REVERT: E 321 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8788 (mt-10) REVERT: E 379 CYS cc_start: 0.9789 (OUTLIER) cc_final: 0.9489 (p) REVERT: E 398 LYS cc_start: 0.9307 (ttpp) cc_final: 0.8903 (ptmm) REVERT: E 418 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8176 (t) REVERT: F 117 MET cc_start: 0.9209 (mmm) cc_final: 0.8522 (mmm) REVERT: F 125 TYR cc_start: 0.8585 (m-80) cc_final: 0.8318 (m-80) REVERT: F 154 LYS cc_start: 0.9370 (mtmm) cc_final: 0.8980 (mtmm) REVERT: F 163 TYR cc_start: 0.9365 (p90) cc_final: 0.8896 (p90) REVERT: F 217 LEU cc_start: 0.9509 (mt) cc_final: 0.9143 (tp) REVERT: F 242 VAL cc_start: 0.9621 (p) cc_final: 0.9291 (m) REVERT: G 7 MET cc_start: 0.9413 (ptm) cc_final: 0.8949 (ppp) REVERT: G 105 GLU cc_start: 0.9041 (pt0) cc_final: 0.8658 (pm20) REVERT: G 112 GLU cc_start: 0.9267 (mp0) cc_final: 0.8728 (pm20) REVERT: G 136 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8652 (m) REVERT: G 152 GLU cc_start: 0.4012 (OUTLIER) cc_final: 0.3616 (tm-30) REVERT: G 386 ASP cc_start: 0.9432 (m-30) cc_final: 0.8779 (t0) REVERT: G 426 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9022 (mm) REVERT: H 68 MET cc_start: 0.8628 (mmm) cc_final: 0.7699 (mmm) REVERT: H 167 HIS cc_start: 0.9368 (OUTLIER) cc_final: 0.9079 (p90) REVERT: H 251 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9087 (ttmm) REVERT: I 178 TYR cc_start: 0.9536 (m-80) cc_final: 0.9185 (m-10) REVERT: I 223 MET cc_start: -0.0031 (ptm) cc_final: -0.0498 (ptp) REVERT: I 314 TRP cc_start: 0.9047 (m-10) cc_final: 0.8743 (m100) REVERT: J 45 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8964 (mm-30) REVERT: J 204 LEU cc_start: 0.9622 (tp) cc_final: 0.9361 (tp) REVERT: J 246 LYS cc_start: 0.9822 (OUTLIER) cc_final: 0.9613 (mtmm) REVERT: K 52 MET cc_start: 0.8603 (mmm) cc_final: 0.8258 (mmm) REVERT: K 302 ASN cc_start: 0.9399 (t0) cc_final: 0.9114 (t0) REVERT: K 309 GLU cc_start: 0.8776 (mp0) cc_final: 0.8570 (mp0) REVERT: L 107 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.5360 (pttm) REVERT: L 125 TYR cc_start: 0.9122 (m-80) cc_final: 0.8865 (m-80) REVERT: L 144 ASP cc_start: 0.9108 (p0) cc_final: 0.8900 (p0) REVERT: L 189 HIS cc_start: 0.9013 (t-90) cc_final: 0.8559 (t70) REVERT: M 9 LEU cc_start: 0.9530 (tp) cc_final: 0.9212 (tp) REVERT: M 41 TYR cc_start: 0.9425 (t80) cc_final: 0.8829 (t80) REVERT: M 49 LEU cc_start: 0.9644 (tt) cc_final: 0.9397 (pp) REVERT: N 6 MET cc_start: 0.9535 (tpp) cc_final: 0.9112 (tpp) REVERT: O 9 LEU cc_start: 0.8238 (tt) cc_final: 0.7990 (tt) REVERT: O 29 ASN cc_start: 0.9397 (OUTLIER) cc_final: 0.9059 (p0) REVERT: O 39 GLN cc_start: 0.9448 (mt0) cc_final: 0.9041 (pt0) REVERT: P 32 GLU cc_start: 0.9209 (pp20) cc_final: 0.8837 (pp20) REVERT: P 35 THR cc_start: 0.9427 (m) cc_final: 0.8953 (p) REVERT: P 36 MET cc_start: 0.9100 (mpp) cc_final: 0.8592 (mpp) REVERT: P 49 LEU cc_start: 0.8860 (tt) cc_final: 0.8430 (tp) REVERT: P 51 ASP cc_start: 0.8959 (m-30) cc_final: 0.8667 (p0) REVERT: R 50 TRP cc_start: 0.8321 (m-10) cc_final: 0.8105 (m-10) outliers start: 205 outliers final: 73 residues processed: 681 average time/residue: 0.2171 time to fit residues: 234.3626 Evaluate side-chains 541 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 448 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 CYS Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain I residue 252 ARG Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 246 LYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 244 TRP Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 29 ASN Chi-restraints excluded: chain O residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 229 optimal weight: 40.0000 chunk 370 optimal weight: 0.0370 chunk 292 optimal weight: 20.0000 chunk 323 optimal weight: 0.5980 chunk 224 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 191 optimal weight: 40.0000 chunk 349 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 164 optimal weight: 30.0000 overall best weight: 3.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 162 HIS ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN E 48 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN F 121 GLN F 168 GLN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN H 41 HIS H 73 GLN H 168 GLN I 176 ASN ** I 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 168 GLN K 338 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.084659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062216 restraints weight = 175890.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063914 restraints weight = 72921.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064451 restraints weight = 47096.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.064419 restraints weight = 44161.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064520 restraints weight = 41443.099| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 34264 Z= 0.168 Angle : 0.815 11.664 46758 Z= 0.408 Chirality : 0.049 0.455 5230 Planarity : 0.007 0.099 5982 Dihedral : 7.016 61.382 4869 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 4.91 % Allowed : 27.99 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.12), residues: 4220 helix: -0.53 (0.21), residues: 539 sheet: -0.59 (0.15), residues: 1174 loop : -1.65 (0.11), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 132 TYR 0.026 0.002 TYR I 216 PHE 0.024 0.002 PHE G 421 TRP 0.027 0.001 TRP C 188 HIS 0.010 0.001 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00378 (34177) covalent geometry : angle 0.80080 (46572) SS BOND : bond 0.00424 ( 75) SS BOND : angle 1.99803 ( 150) hydrogen bonds : bond 0.04008 ( 1152) hydrogen bonds : angle 6.36557 ( 2994) link_NAG-ASN : bond 0.00765 ( 12) link_NAG-ASN : angle 4.06093 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 481 time to evaluate : 0.887 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: A 241 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8218 (m-10) REVERT: A 349 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8772 (mm-30) REVERT: B 233 TRP cc_start: 0.9668 (OUTLIER) cc_final: 0.9239 (t60) REVERT: B 275 HIS cc_start: 0.9416 (OUTLIER) cc_final: 0.9073 (m-70) REVERT: B 386 LEU cc_start: 0.9743 (pp) cc_final: 0.9453 (mm) REVERT: C 125 TYR cc_start: 0.9549 (m-80) cc_final: 0.9276 (m-80) REVERT: C 163 TYR cc_start: 0.9348 (p90) cc_final: 0.9056 (p90) REVERT: C 253 ASP cc_start: 0.8744 (t0) cc_final: 0.8496 (t0) REVERT: D 7 MET cc_start: 0.8760 (tmm) cc_final: 0.8459 (tmm) REVERT: D 421 PHE cc_start: 0.9792 (m-80) cc_final: 0.9502 (t80) REVERT: D 439 HIS cc_start: 0.8798 (m90) cc_final: 0.8482 (m90) REVERT: E 52 MET cc_start: 0.9229 (mmm) cc_final: 0.8953 (mmt) REVERT: E 71 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9340 (ptpp) REVERT: E 208 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9388 (tp) REVERT: E 272 LEU cc_start: 0.9345 (mt) cc_final: 0.9125 (mp) REVERT: E 287 ASP cc_start: 0.9262 (p0) cc_final: 0.8912 (p0) REVERT: E 306 GLN cc_start: 0.8425 (pm20) cc_final: 0.8120 (pm20) REVERT: E 321 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8840 (mt-10) REVERT: E 398 LYS cc_start: 0.9245 (ttpp) cc_final: 0.8831 (ptmm) REVERT: E 418 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8052 (t) REVERT: F 117 MET cc_start: 0.9137 (mmm) cc_final: 0.8875 (mmm) REVERT: F 125 TYR cc_start: 0.8886 (m-80) cc_final: 0.8650 (m-80) REVERT: F 154 LYS cc_start: 0.9327 (mtmm) cc_final: 0.8970 (mtmm) REVERT: F 163 TYR cc_start: 0.9392 (p90) cc_final: 0.8795 (p90) REVERT: F 217 LEU cc_start: 0.9702 (mt) cc_final: 0.9372 (tp) REVERT: G 7 MET cc_start: 0.9386 (ptm) cc_final: 0.8949 (ppp) REVERT: G 105 GLU cc_start: 0.9162 (pt0) cc_final: 0.8598 (pm20) REVERT: G 112 GLU cc_start: 0.9371 (mp0) cc_final: 0.9158 (mp0) REVERT: G 136 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8468 (m) REVERT: G 152 GLU cc_start: 0.3739 (OUTLIER) cc_final: 0.3440 (tm-30) REVERT: G 386 ASP cc_start: 0.9472 (m-30) cc_final: 0.8816 (t0) REVERT: H 68 MET cc_start: 0.8610 (mmm) cc_final: 0.7579 (mmm) REVERT: H 233 TRP cc_start: 0.8818 (OUTLIER) cc_final: 0.8317 (m-10) REVERT: I 178 TYR cc_start: 0.9566 (m-80) cc_final: 0.9138 (m-10) REVERT: I 223 MET cc_start: 0.0125 (ptm) cc_final: -0.0283 (ptp) REVERT: I 253 PHE cc_start: 0.9396 (m-10) cc_final: 0.8960 (m-10) REVERT: I 314 TRP cc_start: 0.8977 (m-10) cc_final: 0.8672 (m100) REVERT: J 10 LYS cc_start: 0.9314 (mmtm) cc_final: 0.9008 (mmtm) REVERT: J 45 GLU cc_start: 0.9378 (mm-30) cc_final: 0.8960 (mm-30) REVERT: J 50 LYS cc_start: 0.9554 (tttm) cc_final: 0.9274 (tptp) REVERT: J 103 MET cc_start: 0.7783 (mmm) cc_final: 0.7371 (mmm) REVERT: J 197 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9017 (mmmm) REVERT: J 246 LYS cc_start: 0.9835 (mtpp) cc_final: 0.9600 (mtmm) REVERT: K 52 MET cc_start: 0.8785 (mmm) cc_final: 0.8424 (mmm) REVERT: K 55 LEU cc_start: 0.9173 (tp) cc_final: 0.8706 (tt) REVERT: K 68 MET cc_start: 0.9007 (mmm) cc_final: 0.8763 (mmm) REVERT: K 171 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8440 (pt) REVERT: K 302 ASN cc_start: 0.9487 (t0) cc_final: 0.9083 (t0) REVERT: K 310 ARG cc_start: 0.8090 (mmm-85) cc_final: 0.7726 (mmm160) REVERT: K 321 GLU cc_start: 0.9307 (mp0) cc_final: 0.9073 (pp20) REVERT: L 107 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.5865 (pttm) REVERT: L 114 PHE cc_start: 0.9471 (m-10) cc_final: 0.9156 (m-10) REVERT: L 117 MET cc_start: 0.9408 (mmm) cc_final: 0.9108 (mmm) REVERT: L 125 TYR cc_start: 0.9090 (m-80) cc_final: 0.8626 (m-80) REVERT: L 134 PHE cc_start: 0.9428 (m-80) cc_final: 0.9098 (m-80) REVERT: L 144 ASP cc_start: 0.9368 (p0) cc_final: 0.9125 (p0) REVERT: L 161 LEU cc_start: 0.9808 (mm) cc_final: 0.9490 (mm) REVERT: L 189 HIS cc_start: 0.9009 (t-90) cc_final: 0.8427 (t70) REVERT: L 190 HIS cc_start: 0.9204 (m-70) cc_final: 0.8871 (m90) REVERT: L 193 VAL cc_start: 0.9685 (OUTLIER) cc_final: 0.9453 (t) REVERT: L 217 LEU cc_start: 0.9528 (mm) cc_final: 0.9201 (tp) REVERT: L 239 LEU cc_start: 0.9258 (mm) cc_final: 0.9058 (pp) REVERT: L 244 TRP cc_start: 0.9137 (m100) cc_final: 0.8239 (m100) REVERT: M 18 GLN cc_start: 0.9603 (pm20) cc_final: 0.9219 (pm20) REVERT: M 29 ASN cc_start: 0.9081 (t0) cc_final: 0.8753 (t0) REVERT: M 37 LEU cc_start: 0.9786 (mm) cc_final: 0.9415 (mm) REVERT: M 41 TYR cc_start: 0.9464 (t80) cc_final: 0.8793 (t80) REVERT: M 55 LYS cc_start: 0.8761 (tptp) cc_final: 0.8490 (tptp) REVERT: N 6 MET cc_start: 0.9717 (tpp) cc_final: 0.9429 (tpp) REVERT: O 22 MET cc_start: 0.8966 (mmp) cc_final: 0.8346 (mmm) REVERT: O 29 ASN cc_start: 0.9253 (p0) cc_final: 0.8998 (p0) REVERT: O 39 GLN cc_start: 0.9468 (mt0) cc_final: 0.9108 (pt0) REVERT: P 6 MET cc_start: 0.9461 (tpp) cc_final: 0.9209 (tpp) REVERT: P 22 MET cc_start: 0.9678 (tpt) cc_final: 0.9231 (mmm) REVERT: P 35 THR cc_start: 0.9428 (m) cc_final: 0.9073 (p) REVERT: P 36 MET cc_start: 0.9312 (mpp) cc_final: 0.8868 (mmt) REVERT: P 49 LEU cc_start: 0.8826 (tt) cc_final: 0.8318 (tp) REVERT: P 51 ASP cc_start: 0.9127 (m-30) cc_final: 0.8902 (p0) outliers start: 180 outliers final: 91 residues processed: 634 average time/residue: 0.2263 time to fit residues: 227.4351 Evaluate side-chains 527 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 423 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 CYS Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 384 TRP Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 298 SER Chi-restraints excluded: chain J residue 321 TYR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 140 GLU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 16 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain P residue 21 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 149 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 403 optimal weight: 50.0000 chunk 182 optimal weight: 9.9990 chunk 178 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 400 optimal weight: 50.0000 chunk 392 optimal weight: 30.0000 chunk 175 optimal weight: 0.9990 chunk 238 optimal weight: 40.0000 chunk 40 optimal weight: 9.9990 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN B 24 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 HIS ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 GLN I 247 GLN ** I 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN K 73 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 ASN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.095083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.084468 restraints weight = 241515.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.083607 restraints weight = 124548.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.083463 restraints weight = 108496.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.083615 restraints weight = 68960.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.083797 restraints weight = 55135.187| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 34264 Z= 0.256 Angle : 0.812 12.443 46758 Z= 0.405 Chirality : 0.048 0.485 5230 Planarity : 0.006 0.095 5982 Dihedral : 6.820 58.882 4867 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.46 % Rotamer: Outliers : 5.46 % Allowed : 27.47 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.12), residues: 4220 helix: -0.25 (0.22), residues: 523 sheet: -0.65 (0.15), residues: 1169 loop : -1.49 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 157 TYR 0.026 0.002 TYR K 397 PHE 0.039 0.002 PHE L 185 TRP 0.029 0.002 TRP C 188 HIS 0.010 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00540 (34177) covalent geometry : angle 0.80004 (46572) SS BOND : bond 0.00460 ( 75) SS BOND : angle 1.85410 ( 150) hydrogen bonds : bond 0.03890 ( 1152) hydrogen bonds : angle 6.23172 ( 2994) link_NAG-ASN : bond 0.00881 ( 12) link_NAG-ASN : angle 3.86061 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 451 time to evaluate : 1.078 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: A 241 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8155 (m-10) REVERT: A 297 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.7898 (p) REVERT: A 349 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8854 (mm-30) REVERT: A 385 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5681 (pptt) REVERT: B 68 MET cc_start: 0.8779 (mmm) cc_final: 0.8551 (mmm) REVERT: B 233 TRP cc_start: 0.9499 (OUTLIER) cc_final: 0.8984 (t60) REVERT: B 292 LEU cc_start: 0.9792 (tp) cc_final: 0.9387 (pp) REVERT: C 125 TYR cc_start: 0.9617 (m-80) cc_final: 0.9381 (m-80) REVERT: C 159 TYR cc_start: 0.9357 (m-80) cc_final: 0.9104 (m-80) REVERT: C 163 TYR cc_start: 0.9554 (p90) cc_final: 0.9294 (p90) REVERT: C 253 ASP cc_start: 0.8909 (t0) cc_final: 0.8528 (p0) REVERT: D 10 LYS cc_start: 0.9609 (mtpt) cc_final: 0.9254 (mtmm) REVERT: D 20 GLU cc_start: 0.8593 (tp30) cc_final: 0.8331 (tp30) REVERT: D 421 PHE cc_start: 0.9780 (m-80) cc_final: 0.9486 (t80) REVERT: D 439 HIS cc_start: 0.8842 (m90) cc_final: 0.8433 (m90) REVERT: E 52 MET cc_start: 0.9211 (mmm) cc_final: 0.8978 (mmt) REVERT: E 65 MET cc_start: 0.9080 (ppp) cc_final: 0.8318 (ppp) REVERT: E 208 ILE cc_start: 0.9678 (OUTLIER) cc_final: 0.9359 (tp) REVERT: E 272 LEU cc_start: 0.9424 (mt) cc_final: 0.9182 (mp) REVERT: E 302 ASN cc_start: 0.9668 (t0) cc_final: 0.9416 (t0) REVERT: E 306 GLN cc_start: 0.8595 (pm20) cc_final: 0.8220 (pm20) REVERT: E 418 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8119 (t) REVERT: F 125 TYR cc_start: 0.9033 (m-80) cc_final: 0.8660 (m-80) REVERT: F 163 TYR cc_start: 0.9474 (p90) cc_final: 0.9027 (p90) REVERT: F 214 ARG cc_start: 0.9520 (tpp-160) cc_final: 0.8794 (tpp80) REVERT: G 7 MET cc_start: 0.9379 (ptm) cc_final: 0.8951 (ppp) REVERT: G 105 GLU cc_start: 0.9117 (pt0) cc_final: 0.8877 (pm20) REVERT: G 135 ILE cc_start: 0.9635 (OUTLIER) cc_final: 0.9431 (mm) REVERT: G 136 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8639 (m) REVERT: G 386 ASP cc_start: 0.9473 (m-30) cc_final: 0.8773 (t0) REVERT: H 68 MET cc_start: 0.8653 (mmm) cc_final: 0.7687 (mmm) REVERT: H 167 HIS cc_start: 0.9477 (OUTLIER) cc_final: 0.9196 (p90) REVERT: H 233 TRP cc_start: 0.8913 (OUTLIER) cc_final: 0.8173 (m-10) REVERT: H 248 PHE cc_start: 0.9278 (m-10) cc_final: 0.9043 (m-80) REVERT: I 178 TYR cc_start: 0.9671 (m-80) cc_final: 0.9277 (m-10) REVERT: I 223 MET cc_start: 0.1404 (ptm) cc_final: 0.0743 (ptp) REVERT: J 10 LYS cc_start: 0.9332 (mmtm) cc_final: 0.9043 (mmtm) REVERT: J 18 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8194 (mm) REVERT: J 37 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8694 (mtm-85) REVERT: J 45 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8987 (mm-30) REVERT: J 79 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.8974 (tp-100) REVERT: J 103 MET cc_start: 0.7454 (mmm) cc_final: 0.7170 (tpt) REVERT: J 197 LYS cc_start: 0.9590 (mmmt) cc_final: 0.9098 (mmmm) REVERT: J 418 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.9023 (t) REVERT: K 52 MET cc_start: 0.8807 (mmm) cc_final: 0.8260 (mmm) REVERT: K 68 MET cc_start: 0.9051 (mmm) cc_final: 0.8741 (mmm) REVERT: K 171 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8922 (pp) REVERT: K 302 ASN cc_start: 0.9548 (t0) cc_final: 0.9169 (t0) REVERT: L 107 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.5840 (ptpp) REVERT: L 125 TYR cc_start: 0.9205 (m-80) cc_final: 0.8750 (m-80) REVERT: L 134 PHE cc_start: 0.9453 (m-80) cc_final: 0.9044 (m-80) REVERT: L 144 ASP cc_start: 0.9476 (p0) cc_final: 0.9275 (p0) REVERT: L 161 LEU cc_start: 0.9856 (OUTLIER) cc_final: 0.9639 (mm) REVERT: L 189 HIS cc_start: 0.8881 (t-90) cc_final: 0.8323 (t70) REVERT: L 190 HIS cc_start: 0.9225 (m-70) cc_final: 0.8931 (m90) REVERT: L 196 GLU cc_start: 0.9298 (pm20) cc_final: 0.9096 (pm20) REVERT: L 217 LEU cc_start: 0.9543 (mm) cc_final: 0.9187 (tp) REVERT: L 244 TRP cc_start: 0.9298 (m100) cc_final: 0.8446 (m100) REVERT: M 6 MET cc_start: 0.9559 (tpp) cc_final: 0.9251 (tpp) REVERT: M 29 ASN cc_start: 0.9094 (t0) cc_final: 0.8742 (t0) REVERT: M 37 LEU cc_start: 0.9751 (mm) cc_final: 0.9240 (tp) REVERT: M 41 TYR cc_start: 0.9608 (t80) cc_final: 0.9016 (t80) REVERT: M 49 LEU cc_start: 0.9340 (pp) cc_final: 0.8992 (pp) REVERT: N 36 MET cc_start: 0.9497 (ptp) cc_final: 0.8783 (ptp) REVERT: N 49 LEU cc_start: 0.9703 (tt) cc_final: 0.9350 (pp) REVERT: O 22 MET cc_start: 0.8622 (mmp) cc_final: 0.7966 (mmm) REVERT: O 29 ASN cc_start: 0.9181 (p0) cc_final: 0.8767 (p0) REVERT: O 32 GLU cc_start: 0.9639 (mp0) cc_final: 0.9366 (mp0) REVERT: O 39 GLN cc_start: 0.9503 (mt0) cc_final: 0.9148 (pt0) REVERT: P 6 MET cc_start: 0.9401 (tpp) cc_final: 0.9073 (tpp) REVERT: P 9 LEU cc_start: 0.8257 (pp) cc_final: 0.7956 (pp) REVERT: P 35 THR cc_start: 0.9544 (m) cc_final: 0.9163 (p) REVERT: P 36 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8732 (mmt) REVERT: P 49 LEU cc_start: 0.8889 (tt) cc_final: 0.8381 (tp) REVERT: R 50 TRP cc_start: 0.8261 (m-10) cc_final: 0.8038 (m-10) outliers start: 200 outliers final: 125 residues processed: 616 average time/residue: 0.2169 time to fit residues: 212.3570 Evaluate side-chains 560 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 416 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 CYS Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 384 TRP Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 257 ARG Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 396 THR Chi-restraints excluded: chain J residue 418 THR Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 95 HIS Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 16 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 36 MET Chi-restraints excluded: chain R residue 67 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 272 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 367 optimal weight: 3.9990 chunk 396 optimal weight: 30.0000 chunk 290 optimal weight: 50.0000 chunk 131 optimal weight: 50.0000 chunk 331 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN H 222 GLN I 247 GLN ** I 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** 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 = 0.4026 r_free = 0.4026 target = 0.096315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.085821 restraints weight = 241630.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.085135 restraints weight = 119636.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.085316 restraints weight = 83516.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.085337 restraints weight = 61513.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.085699 restraints weight = 50679.529| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34264 Z= 0.170 Angle : 0.787 13.357 46758 Z= 0.389 Chirality : 0.049 0.436 5230 Planarity : 0.006 0.088 5982 Dihedral : 6.562 55.909 4867 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.34 % Rotamer: Outliers : 4.88 % Allowed : 28.94 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.12), residues: 4220 helix: -0.12 (0.22), residues: 510 sheet: -0.61 (0.15), residues: 1141 loop : -1.39 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 310 TYR 0.027 0.001 TYR I 216 PHE 0.037 0.002 PHE L 185 TRP 0.029 0.001 TRP C 188 HIS 0.008 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00377 (34177) covalent geometry : angle 0.77513 (46572) SS BOND : bond 0.00389 ( 75) SS BOND : angle 1.67619 ( 150) hydrogen bonds : bond 0.03668 ( 1152) hydrogen bonds : angle 6.09899 ( 2994) link_NAG-ASN : bond 0.00693 ( 12) link_NAG-ASN : angle 3.84626 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 443 time to evaluate : 1.354 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: A 29 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9420 (pp) REVERT: A 88 MET cc_start: 0.9353 (ppp) cc_final: 0.8939 (ppp) REVERT: A 241 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8118 (m-10) REVERT: A 297 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.7921 (p) REVERT: A 349 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8881 (mm-30) REVERT: A 385 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5629 (pptt) REVERT: B 233 TRP cc_start: 0.9464 (OUTLIER) cc_final: 0.8987 (t60) REVERT: C 125 TYR cc_start: 0.9622 (m-80) cc_final: 0.8808 (t80) REVERT: C 145 ASN cc_start: 0.9555 (t0) cc_final: 0.9187 (t0) REVERT: C 155 LYS cc_start: 0.9320 (mmmm) cc_final: 0.8939 (tppt) REVERT: C 163 TYR cc_start: 0.9475 (p90) cc_final: 0.9198 (p90) REVERT: C 253 ASP cc_start: 0.9036 (t0) cc_final: 0.8537 (p0) REVERT: D 7 MET cc_start: 0.8499 (tmm) cc_final: 0.8256 (tmm) REVERT: D 10 LYS cc_start: 0.9590 (mtpt) cc_final: 0.9211 (mtmm) REVERT: D 21 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8317 (tpt170) REVERT: D 421 PHE cc_start: 0.9752 (m-80) cc_final: 0.9466 (t80) REVERT: D 439 HIS cc_start: 0.9012 (m90) cc_final: 0.8689 (m90) REVERT: E 48 GLN cc_start: 0.8950 (tp40) cc_final: 0.8513 (tp40) REVERT: E 65 MET cc_start: 0.9063 (ppp) cc_final: 0.8271 (ppp) REVERT: E 71 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9109 (ptpt) REVERT: E 166 MET cc_start: 0.7974 (pmm) cc_final: 0.7005 (pmm) REVERT: E 208 ILE cc_start: 0.9699 (OUTLIER) cc_final: 0.9408 (tp) REVERT: E 252 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9351 (mp) REVERT: E 272 LEU cc_start: 0.9390 (mt) cc_final: 0.9113 (mp) REVERT: E 302 ASN cc_start: 0.9662 (t0) cc_final: 0.9435 (t0) REVERT: E 306 GLN cc_start: 0.8649 (pm20) cc_final: 0.8238 (pm20) REVERT: E 321 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8725 (mt-10) REVERT: E 379 CYS cc_start: 0.9779 (OUTLIER) cc_final: 0.9504 (p) REVERT: E 398 LYS cc_start: 0.9356 (ttpp) cc_final: 0.8867 (pttp) REVERT: E 418 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8011 (t) REVERT: F 117 MET cc_start: 0.9524 (mmm) cc_final: 0.8835 (mpp) REVERT: F 125 TYR cc_start: 0.8884 (m-80) cc_final: 0.8473 (m-80) REVERT: F 155 LYS cc_start: 0.9480 (mmmm) cc_final: 0.9087 (tppt) REVERT: F 163 TYR cc_start: 0.9381 (p90) cc_final: 0.8997 (p90) REVERT: F 170 MET cc_start: 0.9646 (pmm) cc_final: 0.9315 (pmm) REVERT: F 211 ASP cc_start: 0.9277 (t0) cc_final: 0.7959 (m-30) REVERT: F 217 LEU cc_start: 0.9767 (mm) cc_final: 0.9501 (tp) REVERT: G 7 MET cc_start: 0.9398 (ptm) cc_final: 0.8981 (ppp) REVERT: G 105 GLU cc_start: 0.9077 (pt0) cc_final: 0.8772 (pm20) REVERT: G 132 MET cc_start: 0.9096 (tpp) cc_final: 0.8365 (tpp) REVERT: G 386 ASP cc_start: 0.9496 (m-30) cc_final: 0.8795 (t70) REVERT: H 6 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8745 (t80) REVERT: H 68 MET cc_start: 0.8610 (mmm) cc_final: 0.7774 (mmm) REVERT: H 167 HIS cc_start: 0.9489 (OUTLIER) cc_final: 0.9236 (p90) REVERT: H 233 TRP cc_start: 0.9040 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: H 248 PHE cc_start: 0.9265 (m-10) cc_final: 0.9032 (m-80) REVERT: H 336 TRP cc_start: 0.9302 (m100) cc_final: 0.8812 (m-90) REVERT: I 178 TYR cc_start: 0.9647 (m-80) cc_final: 0.9221 (m-10) REVERT: I 223 MET cc_start: 0.1019 (ptm) cc_final: 0.0399 (ptp) REVERT: J 10 LYS cc_start: 0.9371 (mmtm) cc_final: 0.9055 (mmtm) REVERT: J 18 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8292 (mm) REVERT: J 37 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8673 (mtm-85) REVERT: J 45 GLU cc_start: 0.9377 (mm-30) cc_final: 0.8866 (mm-30) REVERT: J 79 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.8936 (tp-100) REVERT: J 103 MET cc_start: 0.7382 (mmm) cc_final: 0.7101 (tpt) REVERT: J 197 LYS cc_start: 0.9547 (mmmt) cc_final: 0.9043 (mmmm) REVERT: J 418 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8975 (t) REVERT: K 52 MET cc_start: 0.8774 (mmm) cc_final: 0.8202 (mmm) REVERT: K 68 MET cc_start: 0.9053 (mmm) cc_final: 0.8659 (mmm) REVERT: K 171 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8937 (pp) REVERT: K 302 ASN cc_start: 0.9554 (t0) cc_final: 0.9125 (t0) REVERT: K 310 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.8018 (mmm-85) REVERT: K 321 GLU cc_start: 0.9242 (mp0) cc_final: 0.8876 (pp20) REVERT: L 107 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.5895 (ptpp) REVERT: L 117 MET cc_start: 0.9433 (mmm) cc_final: 0.9164 (mmm) REVERT: L 134 PHE cc_start: 0.9490 (m-80) cc_final: 0.9041 (m-80) REVERT: L 161 LEU cc_start: 0.9823 (OUTLIER) cc_final: 0.9566 (mm) REVERT: L 189 HIS cc_start: 0.8841 (t-90) cc_final: 0.8482 (t70) REVERT: L 217 LEU cc_start: 0.9519 (mm) cc_final: 0.9154 (tp) REVERT: L 244 TRP cc_start: 0.9189 (m100) cc_final: 0.8327 (m-10) REVERT: M 6 MET cc_start: 0.9617 (tpp) cc_final: 0.9279 (tpp) REVERT: M 29 ASN cc_start: 0.9102 (t0) cc_final: 0.8753 (t0) REVERT: M 41 TYR cc_start: 0.9584 (t80) cc_final: 0.9007 (t80) REVERT: M 49 LEU cc_start: 0.9279 (pp) cc_final: 0.9013 (pp) REVERT: M 50 LEU cc_start: 0.9809 (tp) cc_final: 0.9607 (tp) REVERT: N 36 MET cc_start: 0.9509 (ptp) cc_final: 0.8730 (ptp) REVERT: N 41 TYR cc_start: 0.9495 (t80) cc_final: 0.9295 (t80) REVERT: N 49 LEU cc_start: 0.9691 (tt) cc_final: 0.9358 (pp) REVERT: O 22 MET cc_start: 0.8500 (mmp) cc_final: 0.7848 (mmm) REVERT: O 29 ASN cc_start: 0.9222 (p0) cc_final: 0.8767 (p0) REVERT: O 32 GLU cc_start: 0.9604 (mp0) cc_final: 0.9357 (mp0) REVERT: O 39 GLN cc_start: 0.9461 (mt0) cc_final: 0.9128 (pt0) REVERT: P 6 MET cc_start: 0.9393 (tpp) cc_final: 0.9045 (tpp) REVERT: P 9 LEU cc_start: 0.8077 (pp) cc_final: 0.7771 (pp) REVERT: P 22 MET cc_start: 0.9063 (mmm) cc_final: 0.8634 (mmm) REVERT: P 35 THR cc_start: 0.9552 (m) cc_final: 0.9151 (p) REVERT: P 36 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8670 (mmt) REVERT: P 49 LEU cc_start: 0.8968 (tt) cc_final: 0.8469 (tp) REVERT: R 50 TRP cc_start: 0.8411 (m-10) cc_final: 0.8174 (m100) outliers start: 179 outliers final: 119 residues processed: 586 average time/residue: 0.2070 time to fit residues: 193.1385 Evaluate side-chains 553 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 412 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 298 SER Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 418 THR Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 11 ASN Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 16 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 36 MET Chi-restraints excluded: chain R residue 67 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 9 optimal weight: 50.0000 chunk 359 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 220 optimal weight: 2.9990 chunk 180 optimal weight: 40.0000 chunk 73 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 407 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 321 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 114 HIS B 253 HIS ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 130 GLN H 346 HIS I 251 ASN ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN L 123 ASN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.093647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.083115 restraints weight = 242053.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.081795 restraints weight = 124787.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.082119 restraints weight = 92388.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.082066 restraints weight = 64000.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.082301 restraints weight = 54155.056| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 34264 Z= 0.256 Angle : 0.818 23.387 46758 Z= 0.403 Chirality : 0.048 0.429 5230 Planarity : 0.006 0.087 5982 Dihedral : 6.525 59.016 4865 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 5.78 % Allowed : 28.21 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.12), residues: 4220 helix: 0.01 (0.22), residues: 509 sheet: -0.69 (0.15), residues: 1141 loop : -1.37 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 310 TYR 0.028 0.002 TYR I 216 PHE 0.035 0.002 PHE L 185 TRP 0.029 0.002 TRP C 188 HIS 0.008 0.001 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00542 (34177) covalent geometry : angle 0.79752 (46572) SS BOND : bond 0.00454 ( 75) SS BOND : angle 1.74951 ( 150) hydrogen bonds : bond 0.03767 ( 1152) hydrogen bonds : angle 6.15410 ( 2994) link_NAG-ASN : bond 0.00780 ( 12) link_NAG-ASN : angle 5.71170 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 428 time to evaluate : 1.228 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: A 29 LEU cc_start: 0.9829 (OUTLIER) cc_final: 0.9444 (pp) REVERT: A 48 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.7456 (m) REVERT: A 88 MET cc_start: 0.9417 (ppp) cc_final: 0.8993 (ppp) REVERT: A 241 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8461 (m-10) REVERT: A 297 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8345 (p) REVERT: A 385 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5789 (pptt) REVERT: B 233 TRP cc_start: 0.9458 (OUTLIER) cc_final: 0.9018 (t60) REVERT: B 274 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8681 (pm20) REVERT: B 280 LEU cc_start: 0.9816 (tp) cc_final: 0.9605 (pt) REVERT: B 281 ILE cc_start: 0.9784 (OUTLIER) cc_final: 0.9507 (pt) REVERT: C 117 MET cc_start: 0.9471 (tpp) cc_final: 0.9129 (tpp) REVERT: C 125 TYR cc_start: 0.9648 (m-80) cc_final: 0.8876 (t80) REVERT: C 127 CYS cc_start: 0.9572 (t) cc_final: 0.9371 (t) REVERT: C 147 GLN cc_start: 0.8905 (pp30) cc_final: 0.8658 (pp30) REVERT: C 163 TYR cc_start: 0.9551 (p90) cc_final: 0.9264 (p90) REVERT: C 253 ASP cc_start: 0.9013 (t0) cc_final: 0.8476 (p0) REVERT: D 7 MET cc_start: 0.8587 (tmm) cc_final: 0.8357 (tmm) REVERT: D 10 LYS cc_start: 0.9608 (mtpt) cc_final: 0.9236 (mtmm) REVERT: D 20 GLU cc_start: 0.8477 (tp30) cc_final: 0.8251 (tp30) REVERT: D 132 MET cc_start: 0.8977 (tpp) cc_final: 0.8616 (tpp) REVERT: D 204 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9278 (mt) REVERT: D 421 PHE cc_start: 0.9772 (m-80) cc_final: 0.9491 (t80) REVERT: D 439 HIS cc_start: 0.9097 (m90) cc_final: 0.8815 (m90) REVERT: E 48 GLN cc_start: 0.8852 (tp40) cc_final: 0.8649 (tp40) REVERT: E 52 MET cc_start: 0.8957 (mmt) cc_final: 0.8408 (mmm) REVERT: E 65 MET cc_start: 0.9141 (ppp) cc_final: 0.8370 (ppp) REVERT: E 71 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9157 (ptpt) REVERT: E 166 MET cc_start: 0.8072 (pmm) cc_final: 0.7670 (pmm) REVERT: E 246 ASP cc_start: 0.8672 (t0) cc_final: 0.8451 (t0) REVERT: E 272 LEU cc_start: 0.9399 (mt) cc_final: 0.9112 (mp) REVERT: E 302 ASN cc_start: 0.9659 (t0) cc_final: 0.9427 (t0) REVERT: E 306 GLN cc_start: 0.8809 (pm20) cc_final: 0.8325 (pm20) REVERT: E 321 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8725 (mt-10) REVERT: E 379 CYS cc_start: 0.9780 (OUTLIER) cc_final: 0.9521 (p) REVERT: E 398 LYS cc_start: 0.9328 (ttpp) cc_final: 0.9048 (pttp) REVERT: E 418 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7991 (t) REVERT: F 155 LYS cc_start: 0.9450 (mmmm) cc_final: 0.9199 (tppt) REVERT: F 163 TYR cc_start: 0.9410 (p90) cc_final: 0.8805 (p90) REVERT: F 169 CYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7360 (p) REVERT: F 170 MET cc_start: 0.9677 (pmm) cc_final: 0.9269 (pmm) REVERT: F 217 LEU cc_start: 0.9796 (mm) cc_final: 0.9477 (tp) REVERT: G 7 MET cc_start: 0.9386 (ptm) cc_final: 0.9040 (ppp) REVERT: G 37 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8751 (mtm-85) REVERT: G 105 GLU cc_start: 0.9156 (pt0) cc_final: 0.8863 (pm20) REVERT: G 136 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8540 (m) REVERT: G 386 ASP cc_start: 0.9510 (m-30) cc_final: 0.8777 (t70) REVERT: H 6 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8680 (t80) REVERT: H 68 MET cc_start: 0.8781 (mmm) cc_final: 0.8167 (mmm) REVERT: H 167 HIS cc_start: 0.9526 (OUTLIER) cc_final: 0.9244 (p90) REVERT: H 233 TRP cc_start: 0.8769 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: H 248 PHE cc_start: 0.9345 (m-10) cc_final: 0.9117 (m-80) REVERT: I 178 TYR cc_start: 0.9698 (m-80) cc_final: 0.9274 (m-10) REVERT: I 223 MET cc_start: 0.1576 (ptm) cc_final: 0.1147 (ptp) REVERT: I 253 PHE cc_start: 0.9117 (m-10) cc_final: 0.8834 (m-10) REVERT: I 292 LEU cc_start: 0.9465 (mm) cc_final: 0.9070 (mm) REVERT: J 10 LYS cc_start: 0.9313 (mmtm) cc_final: 0.9027 (mmtm) REVERT: J 18 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8554 (mm) REVERT: J 45 GLU cc_start: 0.9422 (mm-30) cc_final: 0.8605 (tp30) REVERT: J 79 GLN cc_start: 0.9370 (OUTLIER) cc_final: 0.8957 (tp-100) REVERT: J 103 MET cc_start: 0.7341 (mmm) cc_final: 0.6966 (tpt) REVERT: J 197 LYS cc_start: 0.9593 (mmmt) cc_final: 0.9164 (mmmm) REVERT: J 418 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9067 (t) REVERT: K 52 MET cc_start: 0.8791 (mmm) cc_final: 0.8245 (mmm) REVERT: K 68 MET cc_start: 0.9050 (mmm) cc_final: 0.8684 (mmm) REVERT: K 171 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.8808 (pp) REVERT: K 233 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.8627 (m-10) REVERT: K 302 ASN cc_start: 0.9603 (t0) cc_final: 0.9197 (t0) REVERT: K 321 GLU cc_start: 0.9285 (mp0) cc_final: 0.8969 (pp20) REVERT: L 107 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6078 (ptpp) REVERT: L 134 PHE cc_start: 0.9515 (m-80) cc_final: 0.9036 (m-80) REVERT: L 152 LYS cc_start: 0.9553 (tptt) cc_final: 0.9294 (tptt) REVERT: L 161 LEU cc_start: 0.9843 (OUTLIER) cc_final: 0.9580 (mm) REVERT: L 189 HIS cc_start: 0.8894 (t-90) cc_final: 0.8354 (t70) REVERT: L 190 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8963 (m90) REVERT: L 217 LEU cc_start: 0.9478 (mm) cc_final: 0.9146 (tp) REVERT: L 239 LEU cc_start: 0.9395 (mm) cc_final: 0.9044 (pp) REVERT: L 244 TRP cc_start: 0.9315 (m100) cc_final: 0.8860 (m-10) REVERT: M 37 LEU cc_start: 0.9491 (tp) cc_final: 0.9197 (tp) REVERT: M 41 TYR cc_start: 0.9568 (t80) cc_final: 0.9048 (t80) REVERT: M 49 LEU cc_start: 0.9261 (pp) cc_final: 0.8991 (pp) REVERT: N 41 TYR cc_start: 0.9519 (t80) cc_final: 0.9309 (t80) REVERT: N 49 LEU cc_start: 0.9676 (tt) cc_final: 0.9367 (pp) REVERT: O 22 MET cc_start: 0.8652 (mmp) cc_final: 0.7977 (mmm) REVERT: O 29 ASN cc_start: 0.9186 (p0) cc_final: 0.8799 (p0) REVERT: O 32 GLU cc_start: 0.9601 (mp0) cc_final: 0.9358 (mp0) REVERT: O 39 GLN cc_start: 0.9475 (mt0) cc_final: 0.9119 (pt0) REVERT: P 22 MET cc_start: 0.9091 (mmm) cc_final: 0.8805 (mmm) REVERT: P 35 THR cc_start: 0.9579 (m) cc_final: 0.8969 (p) REVERT: P 36 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8656 (mmt) REVERT: P 39 GLN cc_start: 0.9558 (mm-40) cc_final: 0.8953 (pt0) outliers start: 212 outliers final: 151 residues processed: 597 average time/residue: 0.1992 time to fit residues: 190.2064 Evaluate side-chains 579 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 401 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 272 CYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 396 THR Chi-restraints excluded: chain J residue 418 THR Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 7 CYS Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 11 ASN Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 36 MET Chi-restraints excluded: chain R residue 67 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 88 optimal weight: 0.0270 chunk 102 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 chunk 306 optimal weight: 0.0770 chunk 66 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 189 optimal weight: 8.9990 chunk 327 optimal weight: 30.0000 chunk 177 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN L 119 ASN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.095714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.085338 restraints weight = 241731.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.084086 restraints weight = 121211.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.084452 restraints weight = 88364.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.084392 restraints weight = 63352.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.084663 restraints weight = 53515.086| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34264 Z= 0.149 Angle : 0.807 19.937 46758 Z= 0.393 Chirality : 0.049 0.419 5230 Planarity : 0.006 0.088 5982 Dihedral : 6.353 55.163 4865 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 5.02 % Allowed : 29.27 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.13), residues: 4220 helix: -0.02 (0.23), residues: 510 sheet: -0.73 (0.15), residues: 1221 loop : -1.29 (0.12), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 310 TYR 0.028 0.001 TYR D 24 PHE 0.033 0.001 PHE G 95 TRP 0.029 0.001 TRP C 188 HIS 0.007 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00334 (34177) covalent geometry : angle 0.78978 (46572) SS BOND : bond 0.00301 ( 75) SS BOND : angle 1.47058 ( 150) hydrogen bonds : bond 0.03529 ( 1152) hydrogen bonds : angle 5.99296 ( 2994) link_NAG-ASN : bond 0.00750 ( 12) link_NAG-ASN : angle 5.39331 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 424 time to evaluate : 0.939 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: A 29 LEU cc_start: 0.9823 (OUTLIER) cc_final: 0.9426 (pp) REVERT: A 88 MET cc_start: 0.9482 (ppp) cc_final: 0.9021 (ppp) REVERT: A 241 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8194 (m-10) REVERT: A 297 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8282 (p) REVERT: A 385 LYS cc_start: 0.6266 (OUTLIER) cc_final: 0.6026 (pptt) REVERT: A 439 HIS cc_start: 0.9099 (m90) cc_final: 0.8886 (m90) REVERT: B 128 VAL cc_start: 0.9737 (OUTLIER) cc_final: 0.9521 (m) REVERT: B 233 TRP cc_start: 0.9492 (OUTLIER) cc_final: 0.9104 (t60) REVERT: B 274 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8667 (pm20) REVERT: B 280 LEU cc_start: 0.9826 (tp) cc_final: 0.9623 (pt) REVERT: B 281 ILE cc_start: 0.9788 (OUTLIER) cc_final: 0.9501 (pt) REVERT: C 117 MET cc_start: 0.9449 (tpp) cc_final: 0.9050 (tpp) REVERT: C 125 TYR cc_start: 0.9647 (m-80) cc_final: 0.8864 (t80) REVERT: C 127 CYS cc_start: 0.9578 (t) cc_final: 0.9306 (t) REVERT: C 147 GLN cc_start: 0.8773 (pp30) cc_final: 0.8512 (pp30) REVERT: C 163 TYR cc_start: 0.9501 (p90) cc_final: 0.9129 (p90) REVERT: C 216 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9160 (mp) REVERT: C 253 ASP cc_start: 0.9018 (t0) cc_final: 0.8478 (p0) REVERT: D 7 MET cc_start: 0.8635 (tmm) cc_final: 0.8406 (tmm) REVERT: D 10 LYS cc_start: 0.9628 (mtpt) cc_final: 0.9256 (mtmm) REVERT: D 132 MET cc_start: 0.8900 (tpp) cc_final: 0.8591 (tpp) REVERT: D 204 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9121 (mt) REVERT: D 421 PHE cc_start: 0.9760 (m-80) cc_final: 0.9467 (t80) REVERT: D 439 HIS cc_start: 0.8986 (m90) cc_final: 0.8677 (m90) REVERT: E 48 GLN cc_start: 0.8802 (tp40) cc_final: 0.8527 (tp40) REVERT: E 52 MET cc_start: 0.8907 (mmt) cc_final: 0.8424 (mmm) REVERT: E 65 MET cc_start: 0.9054 (ppp) cc_final: 0.8236 (ppp) REVERT: E 71 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9103 (ptpt) REVERT: E 166 MET cc_start: 0.8041 (pmm) cc_final: 0.7024 (pmm) REVERT: E 208 ILE cc_start: 0.9725 (OUTLIER) cc_final: 0.9438 (tp) REVERT: E 246 ASP cc_start: 0.8715 (t0) cc_final: 0.8505 (t0) REVERT: E 252 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9369 (mp) REVERT: E 272 LEU cc_start: 0.9396 (mt) cc_final: 0.9119 (mp) REVERT: E 302 ASN cc_start: 0.9664 (t0) cc_final: 0.9437 (t0) REVERT: E 306 GLN cc_start: 0.8726 (pm20) cc_final: 0.8236 (pm20) REVERT: E 321 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8733 (mt-10) REVERT: E 397 TYR cc_start: 0.9405 (m-80) cc_final: 0.9118 (m-80) REVERT: E 398 LYS cc_start: 0.9330 (ttpp) cc_final: 0.8972 (ptmm) REVERT: E 418 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7934 (t) REVERT: F 117 MET cc_start: 0.9427 (mmm) cc_final: 0.8683 (mpp) REVERT: F 125 TYR cc_start: 0.8926 (m-80) cc_final: 0.8552 (m-80) REVERT: F 155 LYS cc_start: 0.9405 (mmmm) cc_final: 0.9196 (tppt) REVERT: F 163 TYR cc_start: 0.9322 (p90) cc_final: 0.8624 (p90) REVERT: F 217 LEU cc_start: 0.9775 (mm) cc_final: 0.9487 (tp) REVERT: F 236 ARG cc_start: 0.8752 (tpt170) cc_final: 0.8162 (pmt170) REVERT: G 7 MET cc_start: 0.9385 (ptm) cc_final: 0.8933 (ppp) REVERT: G 132 MET cc_start: 0.9378 (tpp) cc_final: 0.8726 (tpp) REVERT: G 136 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8411 (m) REVERT: G 242 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8877 (pp20) REVERT: G 386 ASP cc_start: 0.9500 (m-30) cc_final: 0.8771 (t70) REVERT: H 6 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8631 (t80) REVERT: H 65 MET cc_start: 0.8556 (tmm) cc_final: 0.8308 (tmm) REVERT: H 167 HIS cc_start: 0.9527 (OUTLIER) cc_final: 0.9234 (p90) REVERT: H 233 TRP cc_start: 0.8752 (OUTLIER) cc_final: 0.8022 (m-10) REVERT: I 178 TYR cc_start: 0.9701 (m-80) cc_final: 0.9273 (m-10) REVERT: I 223 MET cc_start: 0.1359 (ptm) cc_final: 0.0706 (ptp) REVERT: I 253 PHE cc_start: 0.9193 (m-10) cc_final: 0.8811 (m-10) REVERT: J 10 LYS cc_start: 0.9373 (mmtm) cc_final: 0.9075 (mmtm) REVERT: J 18 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8535 (mm) REVERT: J 45 GLU cc_start: 0.9403 (mm-30) cc_final: 0.8632 (tp30) REVERT: J 197 LYS cc_start: 0.9563 (mmmt) cc_final: 0.9090 (mmmm) REVERT: J 418 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9018 (t) REVERT: K 52 MET cc_start: 0.8786 (mmm) cc_final: 0.8232 (mmm) REVERT: K 68 MET cc_start: 0.9005 (mmm) cc_final: 0.8571 (mmm) REVERT: K 171 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8914 (pp) REVERT: K 302 ASN cc_start: 0.9603 (t0) cc_final: 0.9185 (t0) REVERT: K 310 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7986 (mmm-85) REVERT: L 107 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6015 (ptpp) REVERT: L 134 PHE cc_start: 0.9524 (m-80) cc_final: 0.8975 (m-80) REVERT: L 160 ASP cc_start: 0.9562 (t0) cc_final: 0.9309 (t0) REVERT: L 161 LEU cc_start: 0.9819 (OUTLIER) cc_final: 0.9530 (mm) REVERT: L 189 HIS cc_start: 0.8943 (t-90) cc_final: 0.8429 (t70) REVERT: L 217 LEU cc_start: 0.9478 (mm) cc_final: 0.9122 (tp) REVERT: L 239 LEU cc_start: 0.9388 (mm) cc_final: 0.9050 (pp) REVERT: L 242 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.8951 (p) REVERT: L 244 TRP cc_start: 0.9252 (m100) cc_final: 0.8299 (m-10) REVERT: L 252 LYS cc_start: 0.9492 (tppp) cc_final: 0.8913 (tptt) REVERT: M 6 MET cc_start: 0.9521 (tpp) cc_final: 0.9199 (tpp) REVERT: M 41 TYR cc_start: 0.9485 (t80) cc_final: 0.7820 (t80) REVERT: M 49 LEU cc_start: 0.9213 (pp) cc_final: 0.9009 (pp) REVERT: N 36 MET cc_start: 0.9534 (ptp) cc_final: 0.8894 (ptp) REVERT: N 41 TYR cc_start: 0.9480 (t80) cc_final: 0.9227 (t80) REVERT: N 49 LEU cc_start: 0.9653 (tt) cc_final: 0.9330 (pp) REVERT: O 22 MET cc_start: 0.8553 (mmp) cc_final: 0.7879 (mmm) REVERT: O 29 ASN cc_start: 0.9089 (p0) cc_final: 0.8820 (p0) REVERT: O 39 GLN cc_start: 0.9494 (mt0) cc_final: 0.9146 (pt0) REVERT: P 6 MET cc_start: 0.9255 (tpp) cc_final: 0.8645 (tpp) REVERT: P 34 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.5620 (tp) REVERT: P 35 THR cc_start: 0.9601 (m) cc_final: 0.9253 (p) REVERT: P 36 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.8864 (mmt) REVERT: R 50 TRP cc_start: 0.7934 (m-10) cc_final: 0.7677 (m100) outliers start: 184 outliers final: 130 residues processed: 574 average time/residue: 0.2104 time to fit residues: 194.3596 Evaluate side-chains 560 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 404 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 418 THR Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 242 VAL Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 7 CYS Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 16 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 36 MET Chi-restraints excluded: chain R residue 67 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 33 optimal weight: 50.0000 chunk 250 optimal weight: 2.9990 chunk 363 optimal weight: 20.0000 chunk 282 optimal weight: 0.4980 chunk 218 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 299 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 50.0000 chunk 20 optimal weight: 50.0000 overall best weight: 7.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 251 ASN ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN L 119 ASN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.094204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.083657 restraints weight = 242288.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.082379 restraints weight = 123727.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.082677 restraints weight = 93707.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.082604 restraints weight = 66059.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.082890 restraints weight = 55328.222| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 34264 Z= 0.199 Angle : 0.810 15.410 46758 Z= 0.397 Chirality : 0.049 0.421 5230 Planarity : 0.006 0.146 5982 Dihedral : 6.300 55.505 4865 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.16 % Favored : 92.77 % Rotamer: Outliers : 5.10 % Allowed : 29.38 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.13), residues: 4220 helix: -0.10 (0.22), residues: 515 sheet: -0.69 (0.15), residues: 1192 loop : -1.30 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 310 TYR 0.027 0.001 TYR I 216 PHE 0.031 0.002 PHE G 95 TRP 0.049 0.002 TRP K 233 HIS 0.006 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00434 (34177) covalent geometry : angle 0.79820 (46572) SS BOND : bond 0.00360 ( 75) SS BOND : angle 1.79020 ( 150) hydrogen bonds : bond 0.03605 ( 1152) hydrogen bonds : angle 5.96545 ( 2994) link_NAG-ASN : bond 0.00682 ( 12) link_NAG-ASN : angle 3.72623 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 413 time to evaluate : 1.164 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: A 29 LEU cc_start: 0.9829 (OUTLIER) cc_final: 0.9448 (pp) REVERT: A 88 MET cc_start: 0.9586 (ppp) cc_final: 0.9161 (ppp) REVERT: A 241 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8361 (m-80) REVERT: A 297 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8349 (p) REVERT: A 385 LYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5856 (pptt) REVERT: B 128 VAL cc_start: 0.9729 (OUTLIER) cc_final: 0.9516 (m) REVERT: B 233 TRP cc_start: 0.9121 (OUTLIER) cc_final: 0.8452 (t60) REVERT: B 274 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8716 (pm20) REVERT: B 280 LEU cc_start: 0.9846 (tp) cc_final: 0.9605 (pt) REVERT: B 281 ILE cc_start: 0.9799 (OUTLIER) cc_final: 0.9541 (pt) REVERT: C 117 MET cc_start: 0.9604 (tpp) cc_final: 0.9200 (tpp) REVERT: C 125 TYR cc_start: 0.9665 (m-80) cc_final: 0.8906 (t80) REVERT: C 127 CYS cc_start: 0.9604 (t) cc_final: 0.9339 (t) REVERT: C 145 ASN cc_start: 0.9472 (t0) cc_final: 0.9271 (t0) REVERT: C 147 GLN cc_start: 0.8861 (pp30) cc_final: 0.8465 (pp30) REVERT: C 163 TYR cc_start: 0.9538 (p90) cc_final: 0.9166 (p90) REVERT: C 200 PHE cc_start: 0.9212 (m-10) cc_final: 0.8765 (m-10) REVERT: C 216 ILE cc_start: 0.9701 (OUTLIER) cc_final: 0.9218 (mp) REVERT: C 253 ASP cc_start: 0.8987 (t0) cc_final: 0.8327 (p0) REVERT: D 10 LYS cc_start: 0.9619 (mtpt) cc_final: 0.9200 (mtmm) REVERT: D 132 MET cc_start: 0.8917 (tpp) cc_final: 0.8636 (tpp) REVERT: D 204 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9133 (mt) REVERT: D 421 PHE cc_start: 0.9765 (m-80) cc_final: 0.9494 (t80) REVERT: D 439 HIS cc_start: 0.9034 (m90) cc_final: 0.8754 (m90) REVERT: E 48 GLN cc_start: 0.8807 (tp40) cc_final: 0.8568 (tp40) REVERT: E 65 MET cc_start: 0.9070 (ppp) cc_final: 0.8264 (ppp) REVERT: E 71 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.9138 (ptpt) REVERT: E 166 MET cc_start: 0.8056 (pmm) cc_final: 0.7049 (pmm) REVERT: E 208 ILE cc_start: 0.9737 (OUTLIER) cc_final: 0.9465 (tp) REVERT: E 252 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9421 (mp) REVERT: E 272 LEU cc_start: 0.9378 (mt) cc_final: 0.9088 (mp) REVERT: E 302 ASN cc_start: 0.9658 (t0) cc_final: 0.9427 (t0) REVERT: E 306 GLN cc_start: 0.8777 (pm20) cc_final: 0.8313 (pm20) REVERT: E 321 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8700 (mt-10) REVERT: E 379 CYS cc_start: 0.9769 (OUTLIER) cc_final: 0.9511 (p) REVERT: E 397 TYR cc_start: 0.9488 (m-80) cc_final: 0.9241 (m-80) REVERT: E 398 LYS cc_start: 0.9337 (ttpp) cc_final: 0.9005 (ptmm) REVERT: E 418 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7951 (t) REVERT: F 125 TYR cc_start: 0.8946 (m-80) cc_final: 0.8560 (m-80) REVERT: F 163 TYR cc_start: 0.9331 (p90) cc_final: 0.8744 (p90) REVERT: F 217 LEU cc_start: 0.9762 (mm) cc_final: 0.9471 (tp) REVERT: F 236 ARG cc_start: 0.8759 (tpt170) cc_final: 0.8152 (pmt170) REVERT: G 7 MET cc_start: 0.9289 (ptm) cc_final: 0.9000 (ppp) REVERT: G 105 GLU cc_start: 0.9105 (pt0) cc_final: 0.8805 (pm20) REVERT: G 132 MET cc_start: 0.9304 (tpp) cc_final: 0.8936 (tpp) REVERT: G 136 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8445 (m) REVERT: G 386 ASP cc_start: 0.9508 (m-30) cc_final: 0.8791 (t0) REVERT: H 6 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8604 (t80) REVERT: H 68 MET cc_start: 0.8695 (mmm) cc_final: 0.8192 (mmm) REVERT: H 167 HIS cc_start: 0.9533 (OUTLIER) cc_final: 0.9298 (p90) REVERT: I 178 TYR cc_start: 0.9718 (m-80) cc_final: 0.9317 (m-10) REVERT: I 223 MET cc_start: 0.1705 (ptm) cc_final: 0.1242 (ptt) REVERT: I 253 PHE cc_start: 0.9204 (m-10) cc_final: 0.8674 (m-10) REVERT: J 10 LYS cc_start: 0.9341 (mmtm) cc_final: 0.9040 (mmtm) REVERT: J 18 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8613 (mm) REVERT: J 45 GLU cc_start: 0.9413 (mm-30) cc_final: 0.8624 (tp30) REVERT: J 79 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.9058 (tm-30) REVERT: J 197 LYS cc_start: 0.9538 (mmmt) cc_final: 0.9055 (mmmm) REVERT: J 418 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9054 (t) REVERT: K 52 MET cc_start: 0.8843 (mmm) cc_final: 0.8291 (mmm) REVERT: K 68 MET cc_start: 0.9037 (mmm) cc_final: 0.8664 (mmm) REVERT: K 171 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.8781 (pp) REVERT: K 302 ASN cc_start: 0.9606 (t0) cc_final: 0.9203 (t0) REVERT: K 310 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.8009 (mmm-85) REVERT: K 321 GLU cc_start: 0.9275 (pm20) cc_final: 0.8912 (pm20) REVERT: L 107 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6066 (ptpp) REVERT: L 119 ASN cc_start: 0.9357 (OUTLIER) cc_final: 0.9044 (p0) REVERT: L 125 TYR cc_start: 0.9018 (m-80) cc_final: 0.8496 (m-80) REVERT: L 132 ARG cc_start: 0.9729 (ttm110) cc_final: 0.9523 (tpp80) REVERT: L 134 PHE cc_start: 0.9531 (m-80) cc_final: 0.8997 (m-80) REVERT: L 142 ARG cc_start: 0.9613 (ttp80) cc_final: 0.9384 (tmt170) REVERT: L 145 ASN cc_start: 0.9702 (t0) cc_final: 0.9303 (t0) REVERT: L 152 LYS cc_start: 0.9375 (tptt) cc_final: 0.9089 (tptt) REVERT: L 159 TYR cc_start: 0.9321 (m-10) cc_final: 0.8985 (m-10) REVERT: L 160 ASP cc_start: 0.9584 (t0) cc_final: 0.9220 (t0) REVERT: L 161 LEU cc_start: 0.9822 (OUTLIER) cc_final: 0.9516 (mm) REVERT: L 217 LEU cc_start: 0.9459 (mm) cc_final: 0.9104 (tp) REVERT: L 239 LEU cc_start: 0.9445 (mm) cc_final: 0.9097 (mm) REVERT: L 244 TRP cc_start: 0.9319 (m100) cc_final: 0.8854 (m-10) REVERT: L 252 LYS cc_start: 0.9528 (tppp) cc_final: 0.8974 (tptt) REVERT: L 254 THR cc_start: 0.9719 (p) cc_final: 0.9441 (m) REVERT: M 6 MET cc_start: 0.9548 (tpp) cc_final: 0.9252 (tpp) REVERT: M 41 TYR cc_start: 0.9068 (t80) cc_final: 0.8419 (t80) REVERT: N 41 TYR cc_start: 0.9526 (t80) cc_final: 0.9259 (t80) REVERT: N 49 LEU cc_start: 0.9659 (tt) cc_final: 0.9371 (pp) REVERT: O 22 MET cc_start: 0.8639 (mmp) cc_final: 0.7940 (mmm) REVERT: P 6 MET cc_start: 0.9253 (tpp) cc_final: 0.8658 (tpp) REVERT: P 34 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.5792 (tp) REVERT: P 35 THR cc_start: 0.9637 (m) cc_final: 0.9301 (p) REVERT: P 36 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8843 (mmt) REVERT: R 50 TRP cc_start: 0.7881 (m-10) cc_final: 0.7652 (m100) outliers start: 187 outliers final: 143 residues processed: 566 average time/residue: 0.2037 time to fit residues: 185.8759 Evaluate side-chains 568 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 398 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 272 CYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 418 THR Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 243 THR Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 16 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 36 MET Chi-restraints excluded: chain R residue 67 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 330 optimal weight: 50.0000 chunk 249 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 336 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 223 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 31 optimal weight: 50.0000 chunk 181 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 251 ASN ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 GLN L 119 ASN L 123 ASN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.094118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.083657 restraints weight = 242125.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.082293 restraints weight = 123296.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.082590 restraints weight = 92538.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082616 restraints weight = 64061.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.082853 restraints weight = 54553.328| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34264 Z= 0.194 Angle : 0.834 19.355 46758 Z= 0.405 Chirality : 0.049 0.418 5230 Planarity : 0.006 0.120 5982 Dihedral : 6.315 54.994 4865 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.54 % Rotamer: Outliers : 5.13 % Allowed : 29.21 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % 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 aren not related in a simple way. whole: -1.44 (0.13), residues: 4220 helix: -0.07 (0.23), residues: 515 sheet: -0.63 (0.15), residues: 1130 loop : -1.31 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 310 TYR 0.028 0.001 TYR I 216 PHE 0.033 0.002 PHE G 95 TRP 0.064 0.002 TRP K 233 HIS 0.013 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00424 (34177) covalent geometry : angle 0.81812 (46572) SS BOND : bond 0.00377 ( 75) SS BOND : angle 1.62471 ( 150) hydrogen bonds : bond 0.03590 ( 1152) hydrogen bonds : angle 5.96002 ( 2994) link_NAG-ASN : bond 0.00672 ( 12) link_NAG-ASN : angle 5.15209 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 401 time to evaluate : 1.431 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: A 29 LEU cc_start: 0.9810 (OUTLIER) cc_final: 0.9444 (pp) REVERT: A 88 MET cc_start: 0.9579 (ppp) cc_final: 0.9058 (ppp) REVERT: A 241 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: A 297 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8431 (p) REVERT: A 385 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5941 (pptt) REVERT: B 128 VAL cc_start: 0.9725 (OUTLIER) cc_final: 0.9512 (m) REVERT: B 274 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8708 (pm20) REVERT: B 280 LEU cc_start: 0.9848 (tp) cc_final: 0.9591 (pt) REVERT: B 281 ILE cc_start: 0.9797 (OUTLIER) cc_final: 0.9536 (pt) REVERT: C 117 MET cc_start: 0.9532 (tpp) cc_final: 0.8925 (tpp) REVERT: C 125 TYR cc_start: 0.9661 (m-80) cc_final: 0.8886 (t80) REVERT: C 127 CYS cc_start: 0.9599 (t) cc_final: 0.9322 (t) REVERT: C 147 GLN cc_start: 0.8948 (pp30) cc_final: 0.8489 (pp30) REVERT: C 163 TYR cc_start: 0.9527 (p90) cc_final: 0.9142 (p90) REVERT: C 181 LYS cc_start: 0.8899 (mptt) cc_final: 0.8249 (mmtt) REVERT: C 216 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9180 (mp) REVERT: C 253 ASP cc_start: 0.9051 (t0) cc_final: 0.8322 (p0) REVERT: D 10 LYS cc_start: 0.9630 (mtpt) cc_final: 0.9202 (mtmm) REVERT: D 204 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9143 (mt) REVERT: D 421 PHE cc_start: 0.9763 (m-80) cc_final: 0.9492 (t80) REVERT: D 439 HIS cc_start: 0.9071 (m90) cc_final: 0.8819 (m90) REVERT: E 65 MET cc_start: 0.9061 (ppp) cc_final: 0.8263 (ppp) REVERT: E 71 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9123 (ptpt) REVERT: E 166 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7088 (pmm) REVERT: E 208 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9477 (tp) REVERT: E 252 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9433 (mp) REVERT: E 272 LEU cc_start: 0.9388 (mt) cc_final: 0.9097 (mp) REVERT: E 302 ASN cc_start: 0.9653 (t0) cc_final: 0.9428 (t0) REVERT: E 306 GLN cc_start: 0.8792 (pm20) cc_final: 0.8318 (pm20) REVERT: E 321 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8708 (mt-10) REVERT: E 379 CYS cc_start: 0.9766 (OUTLIER) cc_final: 0.9508 (p) REVERT: E 397 TYR cc_start: 0.9498 (m-80) cc_final: 0.9252 (m-80) REVERT: E 398 LYS cc_start: 0.9333 (ttpp) cc_final: 0.8962 (ptmm) REVERT: E 418 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.7977 (t) REVERT: F 132 ARG cc_start: 0.9221 (mmm-85) cc_final: 0.8808 (mmm-85) REVERT: F 134 PHE cc_start: 0.9480 (m-80) cc_final: 0.9216 (m-80) REVERT: F 142 ARG cc_start: 0.9675 (ptm-80) cc_final: 0.9474 (ptm-80) REVERT: F 163 TYR cc_start: 0.9277 (p90) cc_final: 0.8611 (p90) REVERT: F 175 LEU cc_start: 0.9547 (mp) cc_final: 0.9286 (tp) REVERT: F 217 LEU cc_start: 0.9773 (mm) cc_final: 0.9472 (tp) REVERT: F 236 ARG cc_start: 0.8760 (tpt170) cc_final: 0.8144 (pmt170) REVERT: G 7 MET cc_start: 0.9328 (ptm) cc_final: 0.9067 (ppp) REVERT: G 37 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8818 (mtm-85) REVERT: G 105 GLU cc_start: 0.9069 (pt0) cc_final: 0.8847 (pm20) REVERT: G 132 MET cc_start: 0.9310 (tpp) cc_final: 0.9024 (tpp) REVERT: G 136 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8362 (m) REVERT: G 176 ASN cc_start: 0.9665 (m110) cc_final: 0.9336 (p0) REVERT: G 386 ASP cc_start: 0.9504 (m-30) cc_final: 0.8786 (t0) REVERT: H 6 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8509 (t80) REVERT: H 68 MET cc_start: 0.8671 (mmm) cc_final: 0.8163 (mmm) REVERT: H 167 HIS cc_start: 0.9549 (OUTLIER) cc_final: 0.9266 (p90) REVERT: H 233 TRP cc_start: 0.8996 (OUTLIER) cc_final: 0.8436 (m-10) REVERT: I 178 TYR cc_start: 0.9729 (m-80) cc_final: 0.9340 (m-10) REVERT: I 223 MET cc_start: 0.1723 (ptm) cc_final: 0.1246 (ptt) REVERT: I 253 PHE cc_start: 0.9102 (m-10) cc_final: 0.8683 (m-10) REVERT: J 10 LYS cc_start: 0.9332 (mmtm) cc_final: 0.9018 (mmtm) REVERT: J 18 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8617 (mm) REVERT: J 45 GLU cc_start: 0.9404 (mm-30) cc_final: 0.8619 (tp30) REVERT: J 79 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.9028 (tp-100) REVERT: J 103 MET cc_start: 0.8572 (tpp) cc_final: 0.8211 (tpt) REVERT: J 197 LYS cc_start: 0.9541 (mmmt) cc_final: 0.9066 (mmmm) REVERT: J 418 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9059 (t) REVERT: K 52 MET cc_start: 0.8855 (mmm) cc_final: 0.8300 (mmm) REVERT: K 68 MET cc_start: 0.9035 (mmm) cc_final: 0.8652 (mmm) REVERT: K 171 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.8802 (pp) REVERT: K 302 ASN cc_start: 0.9613 (t0) cc_final: 0.9226 (t0) REVERT: K 310 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.8036 (mmm-85) REVERT: L 107 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6085 (ptpp) REVERT: L 132 ARG cc_start: 0.9726 (ttm110) cc_final: 0.9521 (tpp80) REVERT: L 134 PHE cc_start: 0.9537 (m-80) cc_final: 0.9001 (m-80) REVERT: L 159 TYR cc_start: 0.9291 (m-10) cc_final: 0.8937 (m-10) REVERT: L 160 ASP cc_start: 0.9600 (t0) cc_final: 0.9233 (t0) REVERT: L 161 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9440 (mm) REVERT: L 217 LEU cc_start: 0.9505 (mm) cc_final: 0.9085 (tp) REVERT: L 239 LEU cc_start: 0.9527 (mm) cc_final: 0.9230 (mm) REVERT: L 244 TRP cc_start: 0.9309 (m100) cc_final: 0.8778 (m-10) REVERT: L 252 LYS cc_start: 0.9559 (tppp) cc_final: 0.8963 (tptt) REVERT: M 6 MET cc_start: 0.9559 (tpp) cc_final: 0.9258 (tpp) REVERT: M 9 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9197 (mt) REVERT: M 41 TYR cc_start: 0.9058 (t80) cc_final: 0.8417 (t80) REVERT: N 41 TYR cc_start: 0.9541 (t80) cc_final: 0.9244 (t80) REVERT: N 49 LEU cc_start: 0.9648 (tt) cc_final: 0.9342 (pp) REVERT: O 22 MET cc_start: 0.8642 (mmp) cc_final: 0.7938 (mmm) REVERT: O 39 GLN cc_start: 0.9538 (mt0) cc_final: 0.9154 (pt0) REVERT: P 6 MET cc_start: 0.9285 (tpp) cc_final: 0.8697 (tpp) REVERT: P 35 THR cc_start: 0.9660 (m) cc_final: 0.9339 (p) REVERT: P 36 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8859 (mmt) REVERT: R 50 TRP cc_start: 0.7883 (m-10) cc_final: 0.7619 (m100) outliers start: 188 outliers final: 141 residues processed: 551 average time/residue: 0.1958 time to fit residues: 174.9594 Evaluate side-chains 563 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 394 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 272 CYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 418 THR Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 424 LEU Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 176 GLN Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 11 ASN Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 16 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 36 MET Chi-restraints excluded: chain R residue 67 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 267 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 402 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 40.0000 chunk 97 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 413 optimal weight: 0.4980 chunk 250 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 251 ASN ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.093996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.083339 restraints weight = 243600.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.082254 restraints weight = 122551.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.082502 restraints weight = 90859.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.082483 restraints weight = 63417.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.082685 restraints weight = 54112.677| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.247 34264 Z= 0.233 Angle : 0.978 59.189 46758 Z= 0.517 Chirality : 0.051 0.812 5230 Planarity : 0.007 0.198 5982 Dihedral : 6.319 55.009 4865 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer: Outliers : 4.83 % Allowed : 29.62 % Favored : 65.55 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % 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 aren not related in a simple way. whole: -1.43 (0.13), residues: 4220 helix: -0.08 (0.23), residues: 515 sheet: -0.63 (0.15), residues: 1130 loop : -1.30 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.001 ARG C 142 TYR 0.025 0.001 TYR I 216 PHE 0.033 0.001 PHE G 95 TRP 0.064 0.002 TRP K 233 HIS 0.010 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00508 (34177) covalent geometry : angle 0.96220 (46572) SS BOND : bond 0.00449 ( 75) SS BOND : angle 2.14776 ( 150) hydrogen bonds : bond 0.03581 ( 1152) hydrogen bonds : angle 5.96170 ( 2994) link_NAG-ASN : bond 0.00676 ( 12) link_NAG-ASN : angle 5.15035 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8440 Ramachandran restraints generated. 4220 Oldfield, 0 Emsley, 4220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 390 time to evaluate : 1.174 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: A 29 LEU cc_start: 0.9818 (OUTLIER) cc_final: 0.9449 (pp) REVERT: A 88 MET cc_start: 0.9581 (ppp) cc_final: 0.9061 (ppp) REVERT: A 241 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: A 297 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8452 (p) REVERT: A 385 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5981 (pptt) REVERT: B 128 VAL cc_start: 0.9725 (OUTLIER) cc_final: 0.9512 (m) REVERT: B 274 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8753 (pm20) REVERT: B 280 LEU cc_start: 0.9856 (tp) cc_final: 0.9607 (pt) REVERT: B 281 ILE cc_start: 0.9803 (OUTLIER) cc_final: 0.9556 (pt) REVERT: C 125 TYR cc_start: 0.9667 (m-80) cc_final: 0.8903 (t80) REVERT: C 127 CYS cc_start: 0.9600 (t) cc_final: 0.9333 (t) REVERT: C 147 GLN cc_start: 0.8833 (pp30) cc_final: 0.8536 (pp30) REVERT: C 163 TYR cc_start: 0.9516 (p90) cc_final: 0.9133 (p90) REVERT: C 181 LYS cc_start: 0.8945 (mptt) cc_final: 0.8303 (mmtt) REVERT: C 216 ILE cc_start: 0.9712 (OUTLIER) cc_final: 0.9228 (mp) REVERT: C 253 ASP cc_start: 0.9029 (t0) cc_final: 0.8313 (p0) REVERT: D 10 LYS cc_start: 0.9642 (mtpt) cc_final: 0.9206 (mtmm) REVERT: D 204 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9133 (mt) REVERT: D 242 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8730 (mp0) REVERT: D 421 PHE cc_start: 0.9767 (m-80) cc_final: 0.9497 (t80) REVERT: D 439 HIS cc_start: 0.9098 (m90) cc_final: 0.8845 (m90) REVERT: E 65 MET cc_start: 0.9089 (ppp) cc_final: 0.8276 (ppp) REVERT: E 71 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9127 (ptpt) REVERT: E 166 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7071 (pmm) REVERT: E 208 ILE cc_start: 0.9731 (OUTLIER) cc_final: 0.9479 (tp) REVERT: E 252 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9420 (mp) REVERT: E 272 LEU cc_start: 0.9388 (mt) cc_final: 0.9102 (mp) REVERT: E 302 ASN cc_start: 0.9666 (t0) cc_final: 0.9443 (t0) REVERT: E 306 GLN cc_start: 0.8796 (pm20) cc_final: 0.8321 (pm20) REVERT: E 321 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8729 (mt-10) REVERT: E 379 CYS cc_start: 0.9765 (OUTLIER) cc_final: 0.9512 (p) REVERT: E 397 TYR cc_start: 0.9504 (m-80) cc_final: 0.9264 (m-80) REVERT: E 398 LYS cc_start: 0.9318 (ttpp) cc_final: 0.8955 (ptmm) REVERT: E 418 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7915 (t) REVERT: F 132 ARG cc_start: 0.9236 (mmm-85) cc_final: 0.8816 (mmm-85) REVERT: F 134 PHE cc_start: 0.9484 (m-80) cc_final: 0.9218 (m-80) REVERT: F 163 TYR cc_start: 0.9280 (p90) cc_final: 0.8629 (p90) REVERT: F 175 LEU cc_start: 0.9538 (mp) cc_final: 0.9296 (tp) REVERT: F 217 LEU cc_start: 0.9776 (mm) cc_final: 0.9479 (tp) REVERT: F 236 ARG cc_start: 0.8785 (tpt170) cc_final: 0.8168 (pmt170) REVERT: G 7 MET cc_start: 0.9378 (ptm) cc_final: 0.9081 (ppp) REVERT: G 37 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8800 (mtm-85) REVERT: G 105 GLU cc_start: 0.9120 (pt0) cc_final: 0.8844 (pm20) REVERT: G 132 MET cc_start: 0.9336 (tpp) cc_final: 0.9039 (tpp) REVERT: G 136 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8351 (m) REVERT: G 176 ASN cc_start: 0.9681 (m110) cc_final: 0.9342 (p0) REVERT: G 386 ASP cc_start: 0.9519 (m-30) cc_final: 0.8782 (t0) REVERT: H 6 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8565 (t80) REVERT: H 68 MET cc_start: 0.8676 (mmm) cc_final: 0.8170 (mmm) REVERT: H 167 HIS cc_start: 0.9549 (OUTLIER) cc_final: 0.9285 (p90) REVERT: H 233 TRP cc_start: 0.8914 (OUTLIER) cc_final: 0.8376 (m-10) REVERT: I 178 TYR cc_start: 0.9731 (m-80) cc_final: 0.9343 (m-10) REVERT: I 223 MET cc_start: 0.1684 (ptm) cc_final: 0.1210 (ptt) REVERT: I 253 PHE cc_start: 0.9114 (m-10) cc_final: 0.8677 (m-10) REVERT: J 10 LYS cc_start: 0.9328 (mmtm) cc_final: 0.9015 (mmtm) REVERT: J 18 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8634 (mm) REVERT: J 45 GLU cc_start: 0.9436 (mm-30) cc_final: 0.8617 (tp30) REVERT: J 79 GLN cc_start: 0.9517 (OUTLIER) cc_final: 0.9006 (tp-100) REVERT: J 197 LYS cc_start: 0.9561 (mmmt) cc_final: 0.9085 (mmmm) REVERT: J 290 ARG cc_start: 0.9077 (tpp80) cc_final: 0.8864 (tpp80) REVERT: J 418 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9063 (t) REVERT: K 52 MET cc_start: 0.8833 (mmm) cc_final: 0.8291 (mmm) REVERT: K 68 MET cc_start: 0.9049 (mmm) cc_final: 0.8660 (mmm) REVERT: K 127 LYS cc_start: 0.8306 (tptp) cc_final: 0.8009 (tptt) REVERT: K 171 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.8781 (pp) REVERT: K 302 ASN cc_start: 0.9628 (t0) cc_final: 0.9244 (t0) REVERT: K 310 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8047 (mmm-85) REVERT: L 107 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6111 (ptpp) REVERT: L 132 ARG cc_start: 0.9729 (ttm110) cc_final: 0.9519 (tpp80) REVERT: L 134 PHE cc_start: 0.9537 (m-80) cc_final: 0.9002 (m-80) REVERT: L 159 TYR cc_start: 0.9289 (m-10) cc_final: 0.8932 (m-10) REVERT: L 160 ASP cc_start: 0.9600 (t0) cc_final: 0.9225 (t0) REVERT: L 161 LEU cc_start: 0.9796 (OUTLIER) cc_final: 0.9443 (mm) REVERT: L 217 LEU cc_start: 0.9508 (mm) cc_final: 0.9112 (tp) REVERT: L 239 LEU cc_start: 0.9533 (mm) cc_final: 0.9241 (mm) REVERT: L 244 TRP cc_start: 0.9315 (m100) cc_final: 0.8791 (m-10) REVERT: L 252 LYS cc_start: 0.9507 (tppp) cc_final: 0.8965 (tptt) REVERT: M 6 MET cc_start: 0.9560 (tpp) cc_final: 0.9257 (tpp) REVERT: M 9 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9199 (mt) REVERT: M 41 TYR cc_start: 0.9058 (t80) cc_final: 0.8403 (t80) REVERT: N 41 TYR cc_start: 0.9542 (t80) cc_final: 0.9232 (t80) REVERT: N 49 LEU cc_start: 0.9613 (tt) cc_final: 0.9328 (pp) REVERT: O 22 MET cc_start: 0.8700 (mmp) cc_final: 0.7981 (mmm) REVERT: P 6 MET cc_start: 0.9291 (tpp) cc_final: 0.8711 (tpp) REVERT: P 35 THR cc_start: 0.9682 (m) cc_final: 0.9347 (p) REVERT: P 36 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8866 (mmt) REVERT: R 50 TRP cc_start: 0.7864 (m-10) cc_final: 0.7597 (m100) outliers start: 177 outliers final: 142 residues processed: 529 average time/residue: 0.2100 time to fit residues: 179.9339 Evaluate side-chains 554 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 384 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 233 TRP Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 188 TRP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 371 CYS Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 150 CYS Chi-restraints excluded: chain H residue 167 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 233 TRP Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 315 ASN Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 272 CYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 418 THR Chi-restraints excluded: chain J residue 421 PHE Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 233 TRP Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 390 ARG Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 57 ASN Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 11 ASN Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 16 CYS Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 36 MET Chi-restraints excluded: chain R residue 67 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 23 optimal weight: 50.0000 chunk 302 optimal weight: 0.9980 chunk 382 optimal weight: 50.0000 chunk 406 optimal weight: 5.9990 chunk 358 optimal weight: 7.9990 chunk 379 optimal weight: 8.9990 chunk 194 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 380 optimal weight: 10.0000 chunk 363 optimal weight: 40.0000 chunk 120 optimal weight: 0.0570 overall best weight: 4.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 HIS C 121 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS ** J 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.094338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.083917 restraints weight = 241344.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.083355 restraints weight = 114155.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.083434 restraints weight = 73032.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.083507 restraints weight = 59317.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.083949 restraints weight = 49372.406| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34264 Z= 0.169 Angle : 0.848 17.877 46758 Z= 0.411 Chirality : 0.049 0.412 5230 Planarity : 0.006 0.151 5982 Dihedral : 6.268 54.726 4865 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.49 % Favored : 92.46 % Rotamer: Outliers : 4.77 % Allowed : 29.62 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.13), residues: 4220 helix: -0.09 (0.22), residues: 511 sheet: -0.59 (0.15), residues: 1120 loop : -1.30 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 310 TYR 0.028 0.001 TYR I 216 PHE 0.032 0.001 PHE G 95 TRP 0.059 0.002 TRP K 233 HIS 0.012 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00379 (34177) covalent geometry : angle 0.83437 (46572) SS BOND : bond 0.00350 ( 75) SS BOND : angle 1.52110 ( 150) hydrogen bonds : bond 0.03564 ( 1152) hydrogen bonds : angle 5.93222 ( 2994) link_NAG-ASN : bond 0.00698 ( 12) link_NAG-ASN : angle 4.85484 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6556.81 seconds wall clock time: 114 minutes 23.97 seconds (6863.97 seconds total)