Starting phenix.real_space_refine on Sat Jun 28 08:33:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua4_42050/06_2025/8ua4_42050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua4_42050/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ua4_42050/06_2025/8ua4_42050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua4_42050/06_2025/8ua4_42050.map" model { file = "/net/cci-nas-00/data/ceres_data/8ua4_42050/06_2025/8ua4_42050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua4_42050/06_2025/8ua4_42050.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.12, per 1000 atoms: 0.60 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: 8.59 Conformation dependent library (CDL) restraints added in 4.5 seconds 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: 6.00 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: 14.87 Time building geometry restraints manager: 10.29 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 441 or resid 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 441 or resid 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 441 or resid 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 415 or resid 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 415 or re \ sid 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 81.120 Find NCS groups from input model: 2.560 Set up NCS constraints: 0.250 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.620 ------------------------------------------------------------------------------- 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 : 7.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (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 TRP 0.048 0.003 TRP L 244 HIS 0.060 0.003 HIS K 95 PHE 0.085 0.004 PHE B 53 TYR 0.051 0.004 TYR B 98 ARG 0.021 0.001 ARG C 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00914 ( 12) link_NAG-ASN : angle 4.67793 ( 36) hydrogen bonds : bond 0.14532 ( 1152) hydrogen bonds : angle 8.42643 ( 2994) SS BOND : bond 0.08278 ( 75) SS BOND : angle 4.07192 ( 150) covalent geometry : bond 0.01256 (34177) covalent geometry : angle 1.27161 (46572) *********************** 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 : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.6012 time to fit residues: 765.7383 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 : 3.901 ------------------------------------------------------------------------------- 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 355 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 chunk 329 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 200 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 382 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 E 288 HIS ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 GLN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN G 130 GLN H 102 GLN H 168 GLN 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 ** K 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 232 ASN M 31 HIS 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.098869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.088641 restraints weight = 240089.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.087331 restraints weight = 119445.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.087639 restraints weight = 89288.536| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34264 Z= 0.230 Angle : 0.882 12.912 46758 Z= 0.447 Chirality : 0.051 0.493 5230 Planarity : 0.008 0.117 5982 Dihedral : 7.478 64.418 4880 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.59 % Favored : 93.27 % Rotamer: Outliers : 5.89 % Allowed : 28.53 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.67 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.12), residues: 4220 helix: -0.71 (0.21), residues: 535 sheet: -0.70 (0.15), residues: 1155 loop : -1.69 (0.11), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 244 HIS 0.012 0.002 HIS B 181 PHE 0.027 0.002 PHE D 399 TYR 0.025 0.002 TYR I 216 ARG 0.020 0.001 ARG F 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 12) link_NAG-ASN : angle 4.39563 ( 36) hydrogen bonds : bond 0.04375 ( 1152) hydrogen bonds : angle 6.75065 ( 2994) SS BOND : bond 0.00472 ( 75) SS BOND : angle 2.17693 ( 150) covalent geometry : bond 0.00499 (34177) covalent geometry : angle 0.86689 (46572) *********************** 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 733 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 517 time to evaluate : 4.049 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: 0.9166 (OUTLIER) cc_final: 0.8183 (m-10) REVERT: A 349 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8551 (mm-30) REVERT: B 166 MET cc_start: 0.8997 (mtm) cc_final: 0.8690 (mmm) REVERT: B 212 ASP cc_start: 0.9417 (OUTLIER) cc_final: 0.9132 (t0) REVERT: B 275 HIS cc_start: 0.9378 (OUTLIER) cc_final: 0.9124 (m-70) REVERT: B 339 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8592 (tp30) REVERT: B 365 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8973 (mp) REVERT: B 386 LEU cc_start: 0.9782 (pp) cc_final: 0.9497 (mm) REVERT: C 125 TYR cc_start: 0.9500 (m-80) cc_final: 0.9282 (m-80) REVERT: C 145 ASN cc_start: 0.9618 (t0) cc_final: 0.9203 (t0) REVERT: C 218 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.7622 (p0) REVERT: D 243 ARG cc_start: 0.9011 (tmm-80) cc_final: 0.8806 (tmm-80) REVERT: D 421 PHE cc_start: 0.9779 (m-80) cc_final: 0.9480 (t80) REVERT: D 439 HIS cc_start: 0.8631 (m90) cc_final: 0.7982 (m90) REVERT: E 52 MET cc_start: 0.9256 (mmm) cc_final: 0.9053 (mmt) REVERT: E 71 LYS cc_start: 0.9592 (OUTLIER) cc_final: 0.9356 (ptpp) REVERT: E 247 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8093 (p) REVERT: E 270 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8977 (tp30) REVERT: E 287 ASP cc_start: 0.9067 (p0) cc_final: 0.8674 (p0) REVERT: E 306 GLN cc_start: 0.8408 (pm20) cc_final: 0.8154 (pm20) REVERT: E 321 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8813 (mt-10) REVERT: E 379 CYS cc_start: 0.9790 (OUTLIER) cc_final: 0.9500 (p) REVERT: E 418 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8378 (t) REVERT: F 117 MET cc_start: 0.9273 (mmm) cc_final: 0.8813 (mmm) REVERT: F 125 TYR cc_start: 0.8703 (m-80) cc_final: 0.8470 (m-80) REVERT: F 217 LEU cc_start: 0.9553 (mt) cc_final: 0.9189 (tp) REVERT: F 242 VAL cc_start: 0.9669 (p) cc_final: 0.9355 (m) REVERT: G 7 MET cc_start: 0.9411 (ptm) cc_final: 0.9092 (ppp) REVERT: G 105 GLU cc_start: 0.9140 (pt0) cc_final: 0.8901 (pm20) REVERT: G 112 GLU cc_start: 0.9259 (mp0) cc_final: 0.8714 (pm20) REVERT: G 152 GLU cc_start: 0.3782 (OUTLIER) cc_final: 0.3558 (tm-30) REVERT: G 306 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8983 (pm20) REVERT: G 386 ASP cc_start: 0.9426 (m-30) cc_final: 0.8776 (t0) REVERT: H 68 MET cc_start: 0.8971 (mmm) cc_final: 0.8723 (mmm) REVERT: H 167 HIS cc_start: 0.9410 (OUTLIER) cc_final: 0.9143 (p90) REVERT: H 251 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9116 (ttmm) REVERT: I 178 TYR cc_start: 0.9596 (m-80) cc_final: 0.9283 (m-10) REVERT: I 223 MET cc_start: 0.0775 (ptm) cc_final: 0.0163 (ptp) REVERT: I 314 TRP cc_start: 0.9160 (m-10) cc_final: 0.8850 (m100) REVERT: J 10 LYS cc_start: 0.9308 (mmtm) cc_final: 0.9098 (mmtm) REVERT: J 18 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8437 (mm) REVERT: J 45 GLU cc_start: 0.9394 (mm-30) cc_final: 0.8989 (mm-30) REVERT: J 204 LEU cc_start: 0.9641 (tp) cc_final: 0.9374 (tp) REVERT: J 220 LEU cc_start: 0.9726 (tp) cc_final: 0.9513 (tp) REVERT: J 246 LYS cc_start: 0.9812 (OUTLIER) cc_final: 0.9515 (mtmm) REVERT: K 52 MET cc_start: 0.8610 (mmm) cc_final: 0.8206 (mmm) REVERT: K 302 ASN cc_start: 0.9428 (t0) cc_final: 0.9155 (t0) REVERT: K 309 GLU cc_start: 0.8831 (mp0) cc_final: 0.8630 (mp0) REVERT: L 107 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.5627 (pttm) REVERT: L 125 TYR cc_start: 0.9176 (m-80) cc_final: 0.8871 (m-80) REVERT: L 144 ASP cc_start: 0.9208 (p0) cc_final: 0.8925 (p0) REVERT: L 189 HIS cc_start: 0.9075 (t-90) cc_final: 0.8613 (t70) REVERT: M 41 TYR cc_start: 0.9479 (t80) cc_final: 0.8872 (t80) REVERT: M 49 LEU cc_start: 0.9638 (tt) cc_final: 0.9408 (pp) REVERT: N 6 MET cc_start: 0.9581 (tpp) cc_final: 0.9180 (tpp) REVERT: O 11 ASN cc_start: 0.7131 (m-40) cc_final: 0.6861 (m-40) REVERT: O 29 ASN cc_start: 0.9397 (OUTLIER) cc_final: 0.9061 (p0) REVERT: O 39 GLN cc_start: 0.9486 (mt0) cc_final: 0.9054 (pt0) REVERT: P 32 GLU cc_start: 0.9251 (pp20) cc_final: 0.8896 (pp20) REVERT: P 35 THR cc_start: 0.9446 (m) cc_final: 0.9005 (p) REVERT: P 36 MET cc_start: 0.9171 (mpp) cc_final: 0.8652 (mpp) REVERT: P 49 LEU cc_start: 0.8865 (tt) cc_final: 0.8455 (tp) REVERT: P 51 ASP cc_start: 0.9042 (m-30) cc_final: 0.8738 (p0) outliers start: 216 outliers final: 82 residues processed: 701 average time/residue: 0.4826 time to fit residues: 537.1666 Evaluate side-chains 537 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 436 time to evaluate : 5.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 66 THR 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 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 81 LEU 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 125 HIS Chi-restraints excluded: chain D residue 167 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 71 LYS 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 306 GLU Chi-restraints excluded: chain G residue 339 VAL 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 H residue 384 TRP 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 18 LEU 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 172 SER Chi-restraints excluded: chain J residue 203 ASP 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 179 SER 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 N residue 43 SER Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 21 CYS 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 82 optimal weight: 40.0000 chunk 58 optimal weight: 50.0000 chunk 371 optimal weight: 20.0000 chunk 283 optimal weight: 30.0000 chunk 273 optimal weight: 10.0000 chunk 407 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 382 optimal weight: 30.0000 chunk 216 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 291 optimal weight: 40.0000 overall best weight: 11.3996 ------------------------------------------------------------------------------- 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 162 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN ** H 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN H 222 GLN ** I 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 395 HIS K 8 GLN K 73 GLN ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN K 338 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN M 57 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4006 r_free = 0.4006 target = 0.095251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.084670 restraints weight = 242533.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.084100 restraints weight = 118802.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.084208 restraints weight = 80810.319| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 34264 Z= 0.283 Angle : 0.837 12.604 46758 Z= 0.422 Chirality : 0.049 0.468 5230 Planarity : 0.007 0.107 5982 Dihedral : 7.092 62.437 4869 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.14 % Favored : 93.79 % Rotamer: Outliers : 5.65 % Allowed : 27.77 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.12), residues: 4220 helix: -0.27 (0.22), residues: 522 sheet: -0.70 (0.14), residues: 1160 loop : -1.60 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 244 HIS 0.010 0.002 HIS B 181 PHE 0.026 0.002 PHE I 167 TYR 0.024 0.002 TYR I 216 ARG 0.015 0.001 ARG F 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00746 ( 12) link_NAG-ASN : angle 3.97979 ( 36) hydrogen bonds : bond 0.04101 ( 1152) hydrogen bonds : angle 6.45595 ( 2994) SS BOND : bond 0.00511 ( 75) SS BOND : angle 2.12780 ( 150) covalent geometry : bond 0.00598 (34177) covalent geometry : angle 0.82291 (46572) *********************** 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 666 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 459 time to evaluate : 3.871 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: A 241 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8061 (m-10) REVERT: A 349 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8589 (mm-30) REVERT: A 385 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5736 (pptt) REVERT: B 386 LEU cc_start: 0.9750 (pp) cc_final: 0.9494 (mm) REVERT: C 125 TYR cc_start: 0.9554 (m-80) cc_final: 0.9277 (m-80) REVERT: D 246 LYS cc_start: 0.9542 (mmtm) cc_final: 0.9272 (mmtm) REVERT: D 421 PHE cc_start: 0.9766 (m-80) cc_final: 0.9463 (t80) REVERT: D 439 HIS cc_start: 0.8834 (m90) cc_final: 0.8449 (m90) REVERT: E 52 MET cc_start: 0.9249 (mmm) cc_final: 0.8981 (mmt) REVERT: E 65 MET cc_start: 0.9070 (ppp) cc_final: 0.8302 (ppp) REVERT: E 71 LYS cc_start: 0.9615 (OUTLIER) cc_final: 0.9414 (ptpp) REVERT: E 302 ASN cc_start: 0.9666 (t0) cc_final: 0.9441 (t0) REVERT: E 306 GLN cc_start: 0.8606 (pm20) cc_final: 0.8241 (pm20) REVERT: E 379 CYS cc_start: 0.9797 (OUTLIER) cc_final: 0.9529 (p) REVERT: E 398 LYS cc_start: 0.9387 (ttpp) cc_final: 0.8910 (ptmm) REVERT: E 418 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8210 (t) REVERT: F 154 LYS cc_start: 0.9410 (mtmm) cc_final: 0.9081 (mtmm) REVERT: F 163 TYR cc_start: 0.9362 (p90) cc_final: 0.8724 (p90) REVERT: F 217 LEU cc_start: 0.9595 (mt) cc_final: 0.9173 (tp) REVERT: F 242 VAL cc_start: 0.9591 (p) cc_final: 0.9362 (t) REVERT: G 7 MET cc_start: 0.9411 (ptm) cc_final: 0.9206 (ppp) REVERT: G 105 GLU cc_start: 0.9160 (pt0) cc_final: 0.8927 (pm20) REVERT: G 306 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.9002 (pm20) REVERT: H 68 MET cc_start: 0.8922 (mmm) cc_final: 0.8005 (mmm) REVERT: H 167 HIS cc_start: 0.9447 (OUTLIER) cc_final: 0.9123 (p90) REVERT: H 233 TRP cc_start: 0.8749 (OUTLIER) cc_final: 0.8097 (m-10) REVERT: H 251 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.9280 (ttpp) REVERT: I 178 TYR cc_start: 0.9602 (m-80) cc_final: 0.9150 (m-10) REVERT: I 223 MET cc_start: 0.0573 (ptm) cc_final: 0.0019 (ptp) REVERT: I 253 PHE cc_start: 0.9430 (m-10) cc_final: 0.9015 (m-10) REVERT: I 254 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.6984 (p) REVERT: I 297 TRP cc_start: 0.8862 (m-90) cc_final: 0.8587 (m-90) REVERT: I 306 ASP cc_start: 0.9483 (t0) cc_final: 0.9277 (t0) REVERT: J 18 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8678 (mp) REVERT: J 45 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9005 (mm-30) REVERT: J 50 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9199 (tppp) REVERT: J 79 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.8981 (tp-100) REVERT: J 197 LYS cc_start: 0.9625 (mmmt) cc_final: 0.9140 (mmmm) REVERT: J 418 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9054 (t) REVERT: K 52 MET cc_start: 0.8720 (mmm) cc_final: 0.8285 (mmm) REVERT: K 68 MET cc_start: 0.9062 (mmm) cc_final: 0.8820 (mmm) REVERT: K 171 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9013 (pp) REVERT: K 302 ASN cc_start: 0.9521 (t0) cc_final: 0.9189 (t0) REVERT: K 321 GLU cc_start: 0.9309 (mp0) cc_final: 0.9099 (pp20) REVERT: L 107 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.5621 (pttm) REVERT: L 117 MET cc_start: 0.9417 (mmm) cc_final: 0.9148 (mmm) REVERT: L 125 TYR cc_start: 0.9099 (m-80) cc_final: 0.8714 (m-80) REVERT: L 134 PHE cc_start: 0.9401 (m-80) cc_final: 0.9122 (m-80) REVERT: L 161 LEU cc_start: 0.9844 (mm) cc_final: 0.9567 (mm) REVERT: L 189 HIS cc_start: 0.8911 (t-90) cc_final: 0.8346 (t70) REVERT: L 190 HIS cc_start: 0.9205 (m-70) cc_final: 0.8824 (m90) REVERT: L 211 ASP cc_start: 0.8899 (m-30) cc_final: 0.8412 (m-30) REVERT: L 217 LEU cc_start: 0.9508 (mm) cc_final: 0.9177 (tp) REVERT: L 244 TRP cc_start: 0.9131 (m100) cc_final: 0.8209 (m100) REVERT: M 6 MET cc_start: 0.9620 (tpp) cc_final: 0.9339 (tpp) REVERT: M 18 GLN cc_start: 0.9341 (pm20) cc_final: 0.8804 (pm20) REVERT: M 37 LEU cc_start: 0.9856 (mm) cc_final: 0.9563 (tt) REVERT: M 41 TYR cc_start: 0.9619 (t80) cc_final: 0.9081 (t80) REVERT: N 6 MET cc_start: 0.9619 (tpp) cc_final: 0.9229 (tpp) REVERT: O 11 ASN cc_start: 0.7102 (m-40) cc_final: 0.6896 (m-40) REVERT: O 22 MET cc_start: 0.8768 (mmp) cc_final: 0.8193 (mmm) REVERT: O 29 ASN cc_start: 0.9307 (p0) cc_final: 0.8958 (p0) REVERT: O 39 GLN cc_start: 0.9477 (mt0) cc_final: 0.9185 (pt0) REVERT: P 6 MET cc_start: 0.9368 (tpp) cc_final: 0.9035 (tpp) REVERT: P 22 MET cc_start: 0.9407 (tpt) cc_final: 0.8960 (mmm) REVERT: P 32 GLU cc_start: 0.9158 (pp20) cc_final: 0.8891 (pp20) REVERT: P 33 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8528 (p) REVERT: P 35 THR cc_start: 0.9405 (m) cc_final: 0.9036 (p) REVERT: P 36 MET cc_start: 0.9208 (mpp) cc_final: 0.8683 (mpp) REVERT: P 49 LEU cc_start: 0.8986 (tt) cc_final: 0.8464 (tp) REVERT: P 51 ASP cc_start: 0.8925 (m-30) cc_final: 0.8710 (p0) REVERT: R 50 TRP cc_start: 0.8104 (m-10) cc_final: 0.7787 (m100) outliers start: 207 outliers final: 111 residues processed: 638 average time/residue: 0.4889 time to fit residues: 495.1279 Evaluate side-chains 551 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 422 time to evaluate : 4.015 ------------------------------------------------------------------------------- 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 161 LYS 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 377 CYS Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 408 TRP 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 164 VAL Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 315 ASN 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 228 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 125 HIS 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 29 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 128 VAL 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 379 CYS 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 F residue 237 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 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 306 GLU Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 5 HIS Chi-restraints excluded: chain H residue 128 VAL 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 251 LYS 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 H residue 384 TRP Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 257 ARG 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 50 LYS 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 172 SER Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 272 CYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 321 TYR 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 1 ASP Chi-restraints excluded: chain K residue 4 THR 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 247 THR Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain K residue 284 LEU 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 193 VAL Chi-restraints excluded: chain M residue 8 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 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 33 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 198 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 287 optimal weight: 0.1980 chunk 1 optimal weight: 50.0000 chunk 45 optimal weight: 6.9990 chunk 409 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 399 optimal weight: 0.0060 chunk 212 optimal weight: 5.9990 overall best weight: 3.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** 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** E 194 GLN G 130 GLN I 176 ASN I 247 GLN ** I 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 251 ASN K 8 GLN K 114 HIS ** L 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.097406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.086961 restraints weight = 240953.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.085776 restraints weight = 119780.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.086113 restraints weight = 89215.053| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34264 Z= 0.148 Angle : 0.789 13.556 46758 Z= 0.390 Chirality : 0.049 0.438 5230 Planarity : 0.006 0.104 5982 Dihedral : 6.709 59.142 4867 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 4.86 % Allowed : 27.85 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.12), residues: 4220 helix: -0.35 (0.21), residues: 535 sheet: -0.65 (0.15), residues: 1177 loop : -1.56 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 188 HIS 0.009 0.001 HIS H 167 PHE 0.032 0.002 PHE L 185 TYR 0.031 0.002 TYR K 397 ARG 0.015 0.001 ARG F 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 12) link_NAG-ASN : angle 3.86536 ( 36) hydrogen bonds : bond 0.03752 ( 1152) hydrogen bonds : angle 6.18875 ( 2994) SS BOND : bond 0.00326 ( 75) SS BOND : angle 1.65997 ( 150) covalent geometry : bond 0.00334 (34177) covalent geometry : angle 0.77705 (46572) *********************** 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 635 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 457 time to evaluate : 3.552 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: A 161 LYS cc_start: 0.9742 (OUTLIER) cc_final: 0.9470 (mmmt) REVERT: A 241 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8213 (m-10) REVERT: A 297 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 349 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8859 (mm-30) REVERT: A 367 LYS cc_start: 0.9511 (OUTLIER) cc_final: 0.8955 (tptp) REVERT: A 385 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5662 (pptt) REVERT: B 68 MET cc_start: 0.8853 (mmm) cc_final: 0.8551 (mmm) REVERT: B 233 TRP cc_start: 0.9421 (OUTLIER) cc_final: 0.8502 (t60) REVERT: B 292 LEU cc_start: 0.9795 (tp) cc_final: 0.9322 (pp) REVERT: C 125 TYR cc_start: 0.9605 (m-80) cc_final: 0.8767 (t80) REVERT: C 159 TYR cc_start: 0.9581 (m-10) cc_final: 0.9305 (m-10) REVERT: C 160 ASP cc_start: 0.9636 (t0) cc_final: 0.9370 (t0) REVERT: C 218 ASP cc_start: 0.8635 (t70) cc_final: 0.8416 (p0) REVERT: D 7 MET cc_start: 0.8509 (tmm) cc_final: 0.8258 (tmm) REVERT: D 10 LYS cc_start: 0.9597 (mtpt) cc_final: 0.9245 (mtmm) REVERT: D 20 GLU cc_start: 0.8586 (tp30) cc_final: 0.8362 (tp30) REVERT: D 132 MET cc_start: 0.8461 (tpp) cc_final: 0.8238 (tpp) REVERT: D 246 LYS cc_start: 0.9532 (mmtm) cc_final: 0.9217 (mmtm) REVERT: D 421 PHE cc_start: 0.9782 (m-80) cc_final: 0.9486 (t80) REVERT: D 439 HIS cc_start: 0.8967 (m90) cc_final: 0.8587 (m90) REVERT: E 52 MET cc_start: 0.9235 (mmm) cc_final: 0.9008 (mmt) REVERT: E 68 MET cc_start: 0.8872 (mmm) cc_final: 0.8605 (mmm) REVERT: E 166 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7003 (pmm) REVERT: E 252 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9351 (mp) REVERT: E 270 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8762 (tp30) REVERT: E 272 LEU cc_start: 0.9434 (mt) cc_final: 0.9193 (mp) REVERT: E 306 GLN cc_start: 0.8624 (pm20) cc_final: 0.8244 (pm20) REVERT: E 321 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8788 (mt-10) REVERT: E 395 THR cc_start: 0.9791 (OUTLIER) cc_final: 0.9555 (p) REVERT: E 398 LYS cc_start: 0.9369 (ttpp) cc_final: 0.8847 (pttp) REVERT: E 418 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8161 (t) REVERT: F 117 MET cc_start: 0.9441 (mmm) cc_final: 0.8651 (mmm) REVERT: F 154 LYS cc_start: 0.9475 (mtmm) cc_final: 0.9108 (mtmm) REVERT: F 211 ASP cc_start: 0.9290 (t0) cc_final: 0.8966 (m-30) REVERT: F 217 LEU cc_start: 0.9624 (mt) cc_final: 0.9286 (tp) REVERT: G 7 MET cc_start: 0.9338 (ptm) cc_final: 0.9079 (ppp) REVERT: G 20 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8323 (tm-30) REVERT: G 37 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8868 (mtm-85) REVERT: G 105 GLU cc_start: 0.9121 (pt0) cc_final: 0.8751 (pm20) REVERT: G 306 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.9032 (pm20) REVERT: G 386 ASP cc_start: 0.9472 (m-30) cc_final: 0.8754 (t0) REVERT: G 390 ASP cc_start: 0.9249 (p0) cc_final: 0.9030 (p0) REVERT: H 233 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.8319 (m-10) REVERT: H 336 TRP cc_start: 0.9370 (m100) cc_final: 0.8941 (m-90) REVERT: I 178 TYR cc_start: 0.9679 (m-80) cc_final: 0.9281 (m-10) REVERT: I 223 MET cc_start: 0.1297 (ptm) cc_final: 0.0685 (ptp) REVERT: I 253 PHE cc_start: 0.9287 (m-10) cc_final: 0.9074 (m-10) REVERT: I 297 TRP cc_start: 0.8931 (m-90) cc_final: 0.8692 (m-90) REVERT: J 10 LYS cc_start: 0.9314 (mmtm) cc_final: 0.8988 (mmtm) REVERT: J 37 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8616 (mtm-85) REVERT: J 45 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8990 (mm-30) REVERT: J 197 LYS cc_start: 0.9564 (mmmt) cc_final: 0.9030 (mmmm) REVERT: J 204 LEU cc_start: 0.9552 (tp) cc_final: 0.9333 (tp) REVERT: J 290 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8690 (mmp80) REVERT: K 52 MET cc_start: 0.8746 (mmm) cc_final: 0.8233 (mmm) REVERT: K 68 MET cc_start: 0.8994 (mmm) cc_final: 0.8638 (mmm) REVERT: K 171 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8831 (pp) REVERT: K 302 ASN cc_start: 0.9549 (t0) cc_final: 0.9142 (t0) REVERT: K 310 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.8023 (mmm-85) REVERT: L 107 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6024 (ptpp) REVERT: L 114 PHE cc_start: 0.9546 (OUTLIER) cc_final: 0.9334 (m-10) REVERT: L 125 TYR cc_start: 0.9169 (m-80) cc_final: 0.8739 (m-80) REVERT: L 134 PHE cc_start: 0.9412 (m-80) cc_final: 0.9074 (m-80) REVERT: L 161 LEU cc_start: 0.9843 (mm) cc_final: 0.9607 (mm) REVERT: L 189 HIS cc_start: 0.8946 (t-90) cc_final: 0.8524 (t70) REVERT: L 217 LEU cc_start: 0.9560 (mm) cc_final: 0.9215 (tp) REVERT: L 244 TRP cc_start: 0.9282 (m100) cc_final: 0.8391 (m100) REVERT: M 29 ASN cc_start: 0.9086 (t0) cc_final: 0.8717 (t0) REVERT: M 37 LEU cc_start: 0.9720 (mm) cc_final: 0.9204 (tp) REVERT: M 41 TYR cc_start: 0.9580 (t80) cc_final: 0.8880 (t80) REVERT: M 49 LEU cc_start: 0.9578 (tt) cc_final: 0.9117 (pp) REVERT: N 36 MET cc_start: 0.8994 (ptm) cc_final: 0.8637 (ptp) REVERT: N 49 LEU cc_start: 0.9693 (tt) cc_final: 0.9306 (pp) REVERT: O 8 VAL cc_start: 0.9668 (OUTLIER) cc_final: 0.9391 (p) REVERT: O 22 MET cc_start: 0.8757 (mmp) cc_final: 0.8051 (mmm) REVERT: O 29 ASN cc_start: 0.9134 (p0) cc_final: 0.8785 (p0) REVERT: O 32 GLU cc_start: 0.9634 (mp0) cc_final: 0.9373 (mp0) REVERT: O 39 GLN cc_start: 0.9485 (mt0) cc_final: 0.9133 (pt0) REVERT: P 6 MET cc_start: 0.9383 (tpp) cc_final: 0.9047 (tpp) REVERT: P 9 LEU cc_start: 0.8312 (pp) cc_final: 0.8019 (pp) REVERT: P 22 MET cc_start: 0.9575 (tpt) cc_final: 0.9059 (mmm) REVERT: P 32 GLU cc_start: 0.9183 (pp20) cc_final: 0.8927 (pp20) REVERT: P 35 THR cc_start: 0.9496 (m) cc_final: 0.9099 (p) REVERT: P 36 MET cc_start: 0.9248 (mpp) cc_final: 0.8744 (mmt) REVERT: R 50 TRP cc_start: 0.8023 (m-10) cc_final: 0.7615 (m100) outliers start: 178 outliers final: 110 residues processed: 605 average time/residue: 0.4912 time to fit residues: 472.6087 Evaluate side-chains 550 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 420 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 367 LYS 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 22 CYS Chi-restraints excluded: chain B residue 39 ASP 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 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain C residue 121 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 216 ILE 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 87 PHE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR 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 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 128 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 315 ASN Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 137 LEU 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 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 260 CYS Chi-restraints excluded: chain G residue 306 GLU 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 5 HIS 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 171 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 217 CYS 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 H residue 384 TRP Chi-restraints excluded: chain J residue 7 MET 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 167 LEU Chi-restraints excluded: chain J residue 169 SER 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 424 LEU Chi-restraints excluded: chain J residue 438 PHE Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 171 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 L residue 107 LYS Chi-restraints excluded: chain L residue 114 PHE Chi-restraints excluded: chain L residue 118 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 11 ASN Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain O residue 8 VAL 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 33 THR 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 397 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 chunk 387 optimal weight: 8.9990 chunk 5 optimal weight: 50.0000 chunk 144 optimal weight: 8.9990 chunk 21 optimal weight: 50.0000 chunk 71 optimal weight: 30.0000 chunk 295 optimal weight: 50.0000 chunk 355 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** 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 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 GLN I 247 GLN K 102 GLN L 123 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.095443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.084677 restraints weight = 241820.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.083582 restraints weight = 124297.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.083807 restraints weight = 93343.314| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34264 Z= 0.203 Angle : 0.779 11.881 46758 Z= 0.387 Chirality : 0.048 0.429 5230 Planarity : 0.006 0.119 5982 Dihedral : 6.533 56.459 4865 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.66 % Favored : 93.29 % Rotamer: Outliers : 4.80 % Allowed : 28.70 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4220 helix: -0.07 (0.22), residues: 511 sheet: -0.62 (0.15), residues: 1147 loop : -1.40 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 188 HIS 0.016 0.001 HIS A 332 PHE 0.042 0.002 PHE L 185 TYR 0.023 0.001 TYR I 216 ARG 0.016 0.001 ARG F 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 12) link_NAG-ASN : angle 3.62601 ( 36) hydrogen bonds : bond 0.03690 ( 1152) hydrogen bonds : angle 6.10495 ( 2994) SS BOND : bond 0.00404 ( 75) SS BOND : angle 1.75712 ( 150) covalent geometry : bond 0.00440 (34177) covalent geometry : angle 0.76776 (46572) *********************** 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 615 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 439 time to evaluate : 3.933 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: A 29 LEU cc_start: 0.9818 (OUTLIER) cc_final: 0.9432 (pp) REVERT: A 161 LYS cc_start: 0.9729 (OUTLIER) cc_final: 0.9445 (mmmt) REVERT: A 204 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 241 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8232 (m-10) REVERT: A 349 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8990 (mm-30) REVERT: A 367 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.8870 (tptp) REVERT: A 385 LYS cc_start: 0.5799 (OUTLIER) cc_final: 0.5554 (pptt) REVERT: B 280 LEU cc_start: 0.9793 (tp) cc_final: 0.9573 (pt) REVERT: B 281 ILE cc_start: 0.9812 (OUTLIER) cc_final: 0.9535 (tt) REVERT: C 125 TYR cc_start: 0.9617 (m-80) cc_final: 0.8769 (t80) REVERT: C 155 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8849 (tppt) REVERT: C 200 PHE cc_start: 0.9131 (m-10) cc_final: 0.8663 (m-10) REVERT: C 218 ASP cc_start: 0.9127 (t70) cc_final: 0.8817 (p0) REVERT: C 253 ASP cc_start: 0.9367 (t0) cc_final: 0.8771 (t0) REVERT: D 10 LYS cc_start: 0.9575 (mtpt) cc_final: 0.9233 (mtmm) REVERT: D 20 GLU cc_start: 0.8533 (tp30) cc_final: 0.8276 (tp30) REVERT: D 132 MET cc_start: 0.8476 (tpp) cc_final: 0.8262 (tpp) REVERT: D 421 PHE cc_start: 0.9772 (m-80) cc_final: 0.9480 (t80) REVERT: D 439 HIS cc_start: 0.9045 (m90) cc_final: 0.8768 (m90) REVERT: E 48 GLN cc_start: 0.8960 (tp40) cc_final: 0.8593 (tp40) REVERT: E 52 MET cc_start: 0.9227 (mmm) cc_final: 0.8984 (mmt) REVERT: E 166 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7389 (pmm) REVERT: E 246 ASP cc_start: 0.8632 (t0) cc_final: 0.8405 (t0) REVERT: E 270 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8703 (tp30) REVERT: E 272 LEU cc_start: 0.9406 (mt) cc_final: 0.9141 (mp) REVERT: E 306 GLN cc_start: 0.8725 (pm20) cc_final: 0.8285 (pm20) REVERT: E 321 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8745 (mt-10) REVERT: E 395 THR cc_start: 0.9815 (OUTLIER) cc_final: 0.9582 (p) REVERT: E 398 LYS cc_start: 0.9319 (ttpp) cc_final: 0.9060 (pttp) REVERT: E 418 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8130 (t) REVERT: F 117 MET cc_start: 0.9543 (mmm) cc_final: 0.9187 (mmm) REVERT: F 169 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7476 (p) REVERT: F 170 MET cc_start: 0.9645 (pmm) cc_final: 0.9283 (pmm) REVERT: F 211 ASP cc_start: 0.9321 (t0) cc_final: 0.8967 (m-30) REVERT: F 236 ARG cc_start: 0.8710 (tpt170) cc_final: 0.8235 (pmt170) REVERT: G 7 MET cc_start: 0.9281 (ptm) cc_final: 0.9079 (ppp) REVERT: G 20 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8292 (tm-30) REVERT: G 105 GLU cc_start: 0.9132 (pt0) cc_final: 0.8875 (pm20) REVERT: G 136 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8462 (m) REVERT: G 306 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9000 (pm20) REVERT: G 386 ASP cc_start: 0.9472 (m-30) cc_final: 0.8756 (t0) REVERT: H 6 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8823 (t80) REVERT: H 65 MET cc_start: 0.8808 (tmm) cc_final: 0.8506 (tmm) REVERT: H 167 HIS cc_start: 0.9531 (OUTLIER) cc_final: 0.9201 (p90) REVERT: H 233 TRP cc_start: 0.9013 (OUTLIER) cc_final: 0.8399 (m-10) REVERT: H 248 PHE cc_start: 0.9200 (m-10) cc_final: 0.8985 (m-80) REVERT: I 178 TYR cc_start: 0.9680 (m-80) cc_final: 0.9262 (m-10) REVERT: I 223 MET cc_start: 0.1695 (ptm) cc_final: 0.0985 (ptp) REVERT: I 253 PHE cc_start: 0.9079 (m-10) cc_final: 0.8749 (m-10) REVERT: I 297 TRP cc_start: 0.8927 (m-90) cc_final: 0.8715 (m-90) REVERT: J 10 LYS cc_start: 0.9341 (mmtm) cc_final: 0.9061 (mmtm) REVERT: J 45 GLU cc_start: 0.9404 (mm-30) cc_final: 0.8584 (tp30) REVERT: J 79 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.8972 (tp-100) REVERT: J 103 MET cc_start: 0.7607 (mmm) cc_final: 0.7253 (tpt) REVERT: J 197 LYS cc_start: 0.9588 (mmmt) cc_final: 0.9153 (mmmm) REVERT: J 204 LEU cc_start: 0.9603 (tp) cc_final: 0.9385 (tp) REVERT: J 418 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.9004 (t) REVERT: K 52 MET cc_start: 0.8794 (mmm) cc_final: 0.8249 (mmm) REVERT: K 68 MET cc_start: 0.9031 (mmm) cc_final: 0.8665 (mmm) REVERT: K 171 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8947 (pp) REVERT: K 302 ASN cc_start: 0.9540 (t0) cc_final: 0.9119 (t0) REVERT: K 321 GLU cc_start: 0.9288 (mp0) cc_final: 0.8942 (pp20) REVERT: L 107 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6224 (ptpp) REVERT: L 119 ASN cc_start: 0.9316 (t0) cc_final: 0.8859 (t0) REVERT: L 134 PHE cc_start: 0.9438 (m-80) cc_final: 0.9039 (m-80) REVERT: L 161 LEU cc_start: 0.9843 (OUTLIER) cc_final: 0.9618 (mm) REVERT: L 181 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6981 (mmtt) REVERT: L 189 HIS cc_start: 0.8901 (t-90) cc_final: 0.8329 (t70) REVERT: L 190 HIS cc_start: 0.9271 (OUTLIER) cc_final: 0.9069 (m90) REVERT: L 217 LEU cc_start: 0.9543 (mm) cc_final: 0.9202 (tp) REVERT: L 239 LEU cc_start: 0.9318 (mm) cc_final: 0.9062 (pp) REVERT: L 244 TRP cc_start: 0.9203 (m100) cc_final: 0.8580 (m-10) REVERT: M 6 MET cc_start: 0.9582 (tpp) cc_final: 0.9259 (tpp) REVERT: M 29 ASN cc_start: 0.9077 (t0) cc_final: 0.8714 (t0) REVERT: M 41 TYR cc_start: 0.9596 (t80) cc_final: 0.8986 (t80) REVERT: M 49 LEU cc_start: 0.9579 (tt) cc_final: 0.9297 (pp) REVERT: N 49 LEU cc_start: 0.9672 (tt) cc_final: 0.9330 (pp) REVERT: O 8 VAL cc_start: 0.9680 (OUTLIER) cc_final: 0.9405 (p) REVERT: O 22 MET cc_start: 0.8671 (mmp) cc_final: 0.7988 (mmm) REVERT: O 29 ASN cc_start: 0.9174 (p0) cc_final: 0.8773 (p0) REVERT: O 32 GLU cc_start: 0.9601 (mp0) cc_final: 0.9358 (mp0) REVERT: O 36 MET cc_start: 0.8630 (tpt) cc_final: 0.8401 (tpp) REVERT: O 39 GLN cc_start: 0.9519 (mt0) cc_final: 0.9248 (pt0) REVERT: O 40 ASN cc_start: 0.9326 (m-40) cc_final: 0.8366 (m110) REVERT: P 6 MET cc_start: 0.9423 (tpp) cc_final: 0.9085 (tpp) REVERT: P 9 LEU cc_start: 0.8289 (pp) cc_final: 0.7972 (pp) REVERT: P 22 MET cc_start: 0.9547 (tpt) cc_final: 0.8936 (mmm) REVERT: P 32 GLU cc_start: 0.9228 (pp20) cc_final: 0.8934 (pp20) REVERT: P 35 THR cc_start: 0.9523 (m) cc_final: 0.9131 (p) REVERT: P 36 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8770 (mmt) REVERT: P 49 LEU cc_start: 0.8035 (pp) cc_final: 0.7829 (pp) REVERT: R 50 TRP cc_start: 0.7790 (m-10) cc_final: 0.7465 (m100) outliers start: 176 outliers final: 123 residues processed: 583 average time/residue: 0.4885 time to fit residues: 451.7941 Evaluate side-chains 564 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 414 time to evaluate : 3.817 ------------------------------------------------------------------------------- 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 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 204 LEU 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 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 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 263 CYS 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 398 LYS Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 137 LEU 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 193 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR 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 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 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 108 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 270 GLU 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 395 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 169 CYS 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 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 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 306 GLU Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 370 VAL 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 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 H residue 384 TRP 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 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 424 LEU 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 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 118 LEU 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 181 LYS Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 193 VAL 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 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 8 VAL 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 O residue 25 CYS Chi-restraints excluded: chain P residue 21 CYS Chi-restraints excluded: chain P residue 33 THR 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 238 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 96 optimal weight: 40.0000 chunk 239 optimal weight: 20.0000 chunk 295 optimal weight: 50.0000 chunk 304 optimal weight: 30.0000 chunk 218 optimal weight: 40.0000 chunk 351 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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 95 HIS B 114 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** 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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 346 HIS ** L 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3990 r_free = 0.3990 target = 0.093576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.082911 restraints weight = 243617.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.081603 restraints weight = 127383.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.081958 restraints weight = 93527.904| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34264 Z= 0.257 Angle : 0.798 11.913 46758 Z= 0.398 Chirality : 0.048 0.417 5230 Planarity : 0.006 0.093 5982 Dihedral : 6.424 56.482 4865 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 5.65 % Allowed : 28.61 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4220 helix: 0.04 (0.22), residues: 512 sheet: -0.74 (0.15), residues: 1159 loop : -1.40 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 188 HIS 0.015 0.001 HIS A 332 PHE 0.032 0.002 PHE G 95 TYR 0.022 0.002 TYR I 216 ARG 0.014 0.001 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 12) link_NAG-ASN : angle 3.71649 ( 36) hydrogen bonds : bond 0.03749 ( 1152) hydrogen bonds : angle 6.11587 ( 2994) SS BOND : bond 0.00425 ( 75) SS BOND : angle 1.69410 ( 150) covalent geometry : bond 0.00541 (34177) covalent geometry : angle 0.78692 (46572) *********************** 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 635 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 428 time to evaluate : 4.105 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: A 29 LEU cc_start: 0.9826 (OUTLIER) cc_final: 0.9433 (pp) REVERT: A 161 LYS cc_start: 0.9738 (OUTLIER) cc_final: 0.9460 (mmmt) REVERT: A 204 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 241 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8324 (m-10) REVERT: A 290 ARG cc_start: 0.9553 (tpp80) cc_final: 0.9345 (tpp80) REVERT: A 297 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8317 (p) REVERT: A 349 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9128 (mm-30) REVERT: A 367 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.8872 (tptp) REVERT: A 385 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.5660 (pptt) REVERT: B 113 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8834 (t80) REVERT: B 274 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8731 (pm20) REVERT: B 280 LEU cc_start: 0.9831 (tp) cc_final: 0.9616 (pt) REVERT: B 281 ILE cc_start: 0.9801 (OUTLIER) cc_final: 0.9482 (pt) REVERT: B 306 GLN cc_start: 0.9332 (pp30) cc_final: 0.8999 (pm20) REVERT: C 117 MET cc_start: 0.9487 (tpp) cc_final: 0.9208 (tpp) REVERT: C 125 TYR cc_start: 0.9690 (m-80) cc_final: 0.8912 (t80) REVERT: C 250 THR cc_start: 0.9131 (m) cc_final: 0.8861 (p) REVERT: C 253 ASP cc_start: 0.9035 (t0) cc_final: 0.8796 (t0) REVERT: D 10 LYS cc_start: 0.9599 (mtpt) cc_final: 0.9203 (mtmm) REVERT: D 20 GLU cc_start: 0.8456 (tp30) cc_final: 0.8102 (tp30) REVERT: D 421 PHE cc_start: 0.9774 (m-80) cc_final: 0.9487 (t80) REVERT: D 439 HIS cc_start: 0.9079 (m90) cc_final: 0.8839 (m90) REVERT: E 52 MET cc_start: 0.9202 (mmm) cc_final: 0.8820 (mmt) REVERT: E 65 MET cc_start: 0.9129 (ppp) cc_final: 0.8354 (ppp) REVERT: E 166 MET cc_start: 0.8034 (pmm) cc_final: 0.7664 (pmm) REVERT: E 246 ASP cc_start: 0.8736 (t0) cc_final: 0.8513 (t0) REVERT: E 270 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8704 (tp30) REVERT: E 272 LEU cc_start: 0.9419 (mt) cc_final: 0.9147 (mp) REVERT: E 302 ASN cc_start: 0.9666 (t0) cc_final: 0.9443 (t0) REVERT: E 306 GLN cc_start: 0.8839 (pm20) cc_final: 0.8329 (pm20) REVERT: E 321 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8747 (mt-10) REVERT: E 418 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8082 (t) REVERT: F 117 MET cc_start: 0.9576 (mmm) cc_final: 0.8102 (mpp) REVERT: F 142 ARG cc_start: 0.9546 (tmm160) cc_final: 0.9144 (tmm160) REVERT: F 169 CYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7412 (p) REVERT: F 170 MET cc_start: 0.9682 (pmm) cc_final: 0.9378 (pmm) REVERT: F 211 ASP cc_start: 0.9363 (t0) cc_final: 0.9012 (m-30) REVERT: F 217 LEU cc_start: 0.9766 (mm) cc_final: 0.9507 (tp) REVERT: G 7 MET cc_start: 0.9327 (ptm) cc_final: 0.9082 (ppp) REVERT: G 105 GLU cc_start: 0.9165 (pt0) cc_final: 0.8890 (pm20) REVERT: G 136 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8436 (m) REVERT: G 306 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.8992 (pm20) REVERT: G 386 ASP cc_start: 0.9498 (m-30) cc_final: 0.8781 (t70) REVERT: H 6 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8852 (t80) REVERT: H 52 MET cc_start: 0.8606 (mpt) cc_final: 0.8227 (mpp) REVERT: H 65 MET cc_start: 0.8971 (tmm) cc_final: 0.8611 (tmm) REVERT: H 167 HIS cc_start: 0.9557 (OUTLIER) cc_final: 0.9290 (p90) REVERT: H 248 PHE cc_start: 0.9274 (m-10) cc_final: 0.9022 (m-80) REVERT: I 178 TYR cc_start: 0.9702 (m-80) cc_final: 0.9249 (m-10) REVERT: I 223 MET cc_start: 0.1735 (ptm) cc_final: 0.1256 (ptp) REVERT: I 297 TRP cc_start: 0.9010 (m-90) cc_final: 0.8700 (m-90) REVERT: J 10 LYS cc_start: 0.9348 (mmtm) cc_final: 0.9081 (mmtm) REVERT: J 45 GLU cc_start: 0.9413 (mm-30) cc_final: 0.8599 (tp30) REVERT: J 79 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.8934 (tp-100) REVERT: J 103 MET cc_start: 0.7445 (mmm) cc_final: 0.7052 (tpt) REVERT: J 197 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9231 (mmmm) REVERT: J 418 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9067 (t) REVERT: K 52 MET cc_start: 0.8797 (mmm) cc_final: 0.8226 (mmm) REVERT: K 68 MET cc_start: 0.9021 (mmm) cc_final: 0.8617 (mmm) REVERT: K 171 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.8829 (pp) REVERT: K 302 ASN cc_start: 0.9592 (t0) cc_final: 0.9295 (t0) REVERT: K 321 GLU cc_start: 0.9300 (mp0) cc_final: 0.8989 (pp20) REVERT: L 107 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6173 (ptpp) REVERT: L 119 ASN cc_start: 0.9526 (t0) cc_final: 0.9137 (t0) REVERT: L 125 TYR cc_start: 0.9204 (m-80) cc_final: 0.8979 (m-80) REVERT: L 134 PHE cc_start: 0.9466 (m-80) cc_final: 0.9045 (m-80) REVERT: L 161 LEU cc_start: 0.9841 (OUTLIER) cc_final: 0.9565 (mm) REVERT: L 181 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6799 (mmtt) REVERT: L 189 HIS cc_start: 0.8949 (t-90) cc_final: 0.8456 (t70) REVERT: L 217 LEU cc_start: 0.9468 (mm) cc_final: 0.9105 (tp) REVERT: L 222 ARG cc_start: 0.9320 (mtm-85) cc_final: 0.9118 (mtm-85) REVERT: L 239 LEU cc_start: 0.9389 (mm) cc_final: 0.9086 (pp) REVERT: L 244 TRP cc_start: 0.9262 (m100) cc_final: 0.8617 (m-10) REVERT: M 41 TYR cc_start: 0.9599 (t80) cc_final: 0.9055 (t80) REVERT: M 49 LEU cc_start: 0.9578 (tt) cc_final: 0.9266 (pp) REVERT: O 8 VAL cc_start: 0.9647 (OUTLIER) cc_final: 0.9347 (p) REVERT: O 22 MET cc_start: 0.8722 (mmp) cc_final: 0.8031 (mmm) REVERT: O 29 ASN cc_start: 0.9117 (p0) cc_final: 0.8828 (p0) REVERT: O 32 GLU cc_start: 0.9591 (mp0) cc_final: 0.9389 (mp0) REVERT: O 36 MET cc_start: 0.8580 (tpt) cc_final: 0.8318 (tpp) REVERT: O 39 GLN cc_start: 0.9460 (mt0) cc_final: 0.9136 (pt0) REVERT: O 40 ASN cc_start: 0.9343 (m-40) cc_final: 0.8131 (m110) REVERT: P 6 MET cc_start: 0.9467 (tpp) cc_final: 0.9149 (tpp) REVERT: P 9 LEU cc_start: 0.8294 (pp) cc_final: 0.7974 (pp) REVERT: P 22 MET cc_start: 0.9517 (tpt) cc_final: 0.8904 (mmm) REVERT: P 32 GLU cc_start: 0.9245 (pp20) cc_final: 0.8991 (pp20) REVERT: P 35 THR cc_start: 0.9556 (m) cc_final: 0.9170 (p) REVERT: P 36 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8832 (mmt) REVERT: R 50 TRP cc_start: 0.8004 (m-10) cc_final: 0.7748 (m100) outliers start: 207 outliers final: 147 residues processed: 603 average time/residue: 0.4898 time to fit residues: 474.9854 Evaluate side-chains 579 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 406 time to evaluate : 3.772 ------------------------------------------------------------------------------- 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 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 204 LEU 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 297 VAL 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 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 27 CYS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 113 PHE 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 398 LYS Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 413 CYS 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 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 114 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR 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 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 60 VAL Chi-restraints excluded: chain E residue 72 THR 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 177 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 270 GLU 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 151 ILE Chi-restraints excluded: chain F residue 169 CYS 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 222 ARG Chi-restraints excluded: chain F residue 237 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 156 LYS Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 192 GLU 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 306 GLU Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain G residue 370 VAL 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 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 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 384 TRP 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 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 272 CYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 298 SER 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 424 LEU 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 93 SER 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 114 PHE Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 181 LYS 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 32 GLU Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 12 ILE 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 341 optimal weight: 7.9990 chunk 332 optimal weight: 20.0000 chunk 206 optimal weight: 0.8980 chunk 320 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 366 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 254 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 282 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** 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** ** L 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.094813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.084338 restraints weight = 241172.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.083170 restraints weight = 120834.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.083433 restraints weight = 89952.100| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34264 Z= 0.173 Angle : 0.806 24.964 46758 Z= 0.393 Chirality : 0.049 0.434 5230 Planarity : 0.006 0.093 5982 Dihedral : 6.387 58.454 4865 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 4.99 % Allowed : 29.43 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4220 helix: 0.02 (0.22), residues: 518 sheet: -0.72 (0.15), residues: 1144 loop : -1.37 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 188 HIS 0.015 0.001 HIS A 332 PHE 0.032 0.002 PHE G 95 TYR 0.023 0.001 TYR I 216 ARG 0.016 0.001 ARG B 390 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 12) link_NAG-ASN : angle 5.97773 ( 36) hydrogen bonds : bond 0.03559 ( 1152) hydrogen bonds : angle 5.99312 ( 2994) SS BOND : bond 0.00331 ( 75) SS BOND : angle 1.48142 ( 150) covalent geometry : bond 0.00379 (34177) covalent geometry : angle 0.78615 (46572) *********************** 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 616 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 433 time to evaluate : 3.898 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: 0.9824 (OUTLIER) cc_final: 0.9456 (pp) REVERT: A 88 MET cc_start: 0.9502 (ppp) cc_final: 0.9277 (ppp) REVERT: A 161 LYS cc_start: 0.9742 (OUTLIER) cc_final: 0.9489 (mmmt) REVERT: A 204 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8324 (mt) REVERT: A 241 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8285 (m-10) REVERT: A 297 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8405 (p) REVERT: A 349 GLU cc_start: 0.9439 (OUTLIER) cc_final: 0.9227 (mm-30) REVERT: A 385 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5765 (pptt) REVERT: B 113 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8866 (t80) REVERT: B 128 VAL cc_start: 0.9758 (OUTLIER) cc_final: 0.9552 (m) REVERT: B 274 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8753 (pm20) REVERT: B 280 LEU cc_start: 0.9840 (tp) cc_final: 0.9595 (pt) REVERT: B 281 ILE cc_start: 0.9799 (OUTLIER) cc_final: 0.9494 (pt) REVERT: B 306 GLN cc_start: 0.9203 (pp30) cc_final: 0.8801 (pm20) REVERT: C 117 MET cc_start: 0.9404 (tpp) cc_final: 0.9128 (tpp) REVERT: C 121 GLN cc_start: 0.9728 (OUTLIER) cc_final: 0.9323 (pm20) REVERT: C 125 TYR cc_start: 0.9705 (m-80) cc_final: 0.8955 (t80) REVERT: C 155 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8843 (tppt) REVERT: C 250 THR cc_start: 0.8944 (m) cc_final: 0.8725 (p) REVERT: C 253 ASP cc_start: 0.8930 (t0) cc_final: 0.8636 (t0) REVERT: D 7 MET cc_start: 0.8643 (tmm) cc_final: 0.8041 (tmm) REVERT: D 10 LYS cc_start: 0.9607 (mtpt) cc_final: 0.9219 (mtmm) REVERT: D 20 GLU cc_start: 0.8356 (tp30) cc_final: 0.8081 (tp30) REVERT: D 421 PHE cc_start: 0.9772 (m-80) cc_final: 0.9489 (t80) REVERT: D 439 HIS cc_start: 0.9017 (m90) cc_final: 0.8702 (m90) REVERT: E 52 MET cc_start: 0.9209 (mmm) cc_final: 0.8846 (mmt) REVERT: E 65 MET cc_start: 0.9064 (ppp) cc_final: 0.8265 (ppp) REVERT: E 71 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8778 (ptpt) REVERT: E 166 MET cc_start: 0.8060 (pmm) cc_final: 0.7719 (pmm) REVERT: E 272 LEU cc_start: 0.9420 (mt) cc_final: 0.9124 (mp) REVERT: E 302 ASN cc_start: 0.9680 (t0) cc_final: 0.9453 (t0) REVERT: E 306 GLN cc_start: 0.8810 (pm20) cc_final: 0.8328 (pm20) REVERT: E 321 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8755 (mt-10) REVERT: E 398 LYS cc_start: 0.9410 (ttpp) cc_final: 0.9141 (pttp) REVERT: E 418 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8033 (t) REVERT: F 211 ASP cc_start: 0.9353 (t0) cc_final: 0.8956 (m-30) REVERT: F 217 LEU cc_start: 0.9793 (mm) cc_final: 0.9435 (tp) REVERT: G 7 MET cc_start: 0.9312 (ptm) cc_final: 0.9020 (ppp) REVERT: G 105 GLU cc_start: 0.9182 (pt0) cc_final: 0.8810 (pm20) REVERT: G 132 MET cc_start: 0.9090 (tpp) cc_final: 0.8575 (tpp) REVERT: G 136 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8290 (m) REVERT: G 306 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9018 (pm20) REVERT: H 65 MET cc_start: 0.9071 (tmm) cc_final: 0.8635 (tmm) REVERT: H 167 HIS cc_start: 0.9558 (OUTLIER) cc_final: 0.9301 (p90) REVERT: H 248 PHE cc_start: 0.9276 (m-10) cc_final: 0.9027 (m-80) REVERT: I 178 TYR cc_start: 0.9731 (m-80) cc_final: 0.9333 (m-10) REVERT: I 223 MET cc_start: 0.1878 (ptm) cc_final: 0.1357 (ptt) REVERT: I 253 PHE cc_start: 0.8973 (m-10) cc_final: 0.8475 (m-10) REVERT: I 297 TRP cc_start: 0.8999 (m-90) cc_final: 0.8766 (m-90) REVERT: J 10 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9066 (mmtm) REVERT: J 45 GLU cc_start: 0.9445 (mm-30) cc_final: 0.8628 (tp30) REVERT: J 79 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.8988 (tp-100) REVERT: J 197 LYS cc_start: 0.9604 (mmmt) cc_final: 0.9150 (mmmm) REVERT: J 418 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.9058 (t) REVERT: K 52 MET cc_start: 0.8849 (mmm) cc_final: 0.8288 (mmm) REVERT: K 68 MET cc_start: 0.9034 (mmm) cc_final: 0.8580 (mmm) REVERT: K 171 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.8800 (pp) REVERT: K 302 ASN cc_start: 0.9608 (t0) cc_final: 0.9312 (t0) REVERT: L 107 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6200 (ptpp) REVERT: L 119 ASN cc_start: 0.9463 (t0) cc_final: 0.9121 (t0) REVERT: L 134 PHE cc_start: 0.9487 (m-80) cc_final: 0.9020 (m-80) REVERT: L 159 TYR cc_start: 0.9200 (m-10) cc_final: 0.8857 (m-10) REVERT: L 160 ASP cc_start: 0.9582 (t0) cc_final: 0.9341 (t0) REVERT: L 161 LEU cc_start: 0.9817 (OUTLIER) cc_final: 0.9580 (mm) REVERT: L 217 LEU cc_start: 0.9418 (mm) cc_final: 0.9045 (tp) REVERT: L 239 LEU cc_start: 0.9403 (mm) cc_final: 0.9070 (pp) REVERT: L 241 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.8551 (t) REVERT: L 242 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8941 (p) REVERT: L 244 TRP cc_start: 0.9272 (m100) cc_final: 0.8720 (m-10) REVERT: L 252 LYS cc_start: 0.9589 (tppp) cc_final: 0.8724 (tptt) REVERT: L 254 THR cc_start: 0.9709 (p) cc_final: 0.9270 (t) REVERT: M 6 MET cc_start: 0.9536 (tpp) cc_final: 0.9231 (tpp) REVERT: M 41 TYR cc_start: 0.9529 (t80) cc_final: 0.9009 (t80) REVERT: M 49 LEU cc_start: 0.9608 (tt) cc_final: 0.9328 (pp) REVERT: N 42 ASP cc_start: 0.9426 (m-30) cc_final: 0.9124 (m-30) REVERT: O 8 VAL cc_start: 0.9646 (OUTLIER) cc_final: 0.9359 (p) REVERT: O 9 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8003 (tt) REVERT: O 22 MET cc_start: 0.8651 (mmp) cc_final: 0.7947 (mmm) REVERT: O 29 ASN cc_start: 0.9026 (p0) cc_final: 0.8810 (p0) REVERT: O 36 MET cc_start: 0.8627 (tpt) cc_final: 0.8351 (tpp) REVERT: O 39 GLN cc_start: 0.9475 (mt0) cc_final: 0.9180 (pt0) REVERT: O 40 ASN cc_start: 0.9354 (m-40) cc_final: 0.8178 (m110) REVERT: P 6 MET cc_start: 0.9461 (tpp) cc_final: 0.9142 (tpp) REVERT: P 9 LEU cc_start: 0.8392 (pp) cc_final: 0.8130 (pp) REVERT: P 22 MET cc_start: 0.9469 (tpt) cc_final: 0.8806 (mmm) REVERT: P 32 GLU cc_start: 0.9352 (pp20) cc_final: 0.9042 (pp20) REVERT: P 35 THR cc_start: 0.9632 (m) cc_final: 0.9263 (p) REVERT: P 36 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8904 (mmt) REVERT: R 50 TRP cc_start: 0.7913 (m-10) cc_final: 0.7711 (m100) outliers start: 183 outliers final: 131 residues processed: 584 average time/residue: 0.4649 time to fit residues: 436.5507 Evaluate side-chains 563 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 405 time to evaluate : 3.216 ------------------------------------------------------------------------------- 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 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 204 LEU 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 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 438 PHE 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 113 PHE 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 315 ASN Chi-restraints excluded: chain B residue 321 GLU 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 121 GLN 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 63 CYS Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR 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 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 45 ILE 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 108 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 270 GLU 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 178 THR Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 228 LEU 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 136 THR Chi-restraints excluded: chain G residue 156 LYS 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 306 GLU Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain G residue 398 SER 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 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 384 TRP 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 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 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 44 VAL Chi-restraints excluded: chain K residue 99 ILE 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 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 161 LEU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 241 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 37 LEU Chi-restraints excluded: chain M residue 43 SER 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 8 VAL Chi-restraints excluded: chain O residue 9 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 296 optimal weight: 9.9990 chunk 163 optimal weight: 40.0000 chunk 339 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 397 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 130 optimal weight: 40.0000 chunk 406 optimal weight: 20.0000 chunk 350 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** 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 138 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 ASN ** L 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.093723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.082999 restraints weight = 242056.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.082564 restraints weight = 109540.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.082528 restraints weight = 86346.697| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 34264 Z= 0.215 Angle : 0.816 18.543 46758 Z= 0.401 Chirality : 0.048 0.418 5230 Planarity : 0.006 0.092 5982 Dihedral : 6.382 55.733 4865 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.65 % Rotamer: Outliers : 4.83 % Allowed : 30.11 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4220 helix: 0.06 (0.23), residues: 511 sheet: -0.69 (0.15), residues: 1117 loop : -1.38 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 188 HIS 0.014 0.001 HIS A 332 PHE 0.038 0.002 PHE G 421 TYR 0.025 0.001 TYR E 98 ARG 0.013 0.001 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 12) link_NAG-ASN : angle 4.99584 ( 36) hydrogen bonds : bond 0.03635 ( 1152) hydrogen bonds : angle 5.98509 ( 2994) SS BOND : bond 0.00554 ( 75) SS BOND : angle 1.66551 ( 150) covalent geometry : bond 0.00464 (34177) covalent geometry : angle 0.79974 (46572) *********************** 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 594 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 417 time to evaluate : 4.046 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: A 29 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9405 (pp) REVERT: A 88 MET cc_start: 0.9515 (ppp) cc_final: 0.9177 (ppp) REVERT: A 204 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8252 (mt) REVERT: A 241 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: A 297 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 349 GLU cc_start: 0.9454 (OUTLIER) cc_final: 0.9213 (mm-30) REVERT: A 385 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5816 (pptt) REVERT: B 113 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8848 (t80) REVERT: B 128 VAL cc_start: 0.9744 (OUTLIER) cc_final: 0.9532 (m) REVERT: B 274 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: B 280 LEU cc_start: 0.9809 (tp) cc_final: 0.9512 (pt) REVERT: B 281 ILE cc_start: 0.9783 (OUTLIER) cc_final: 0.9581 (pt) REVERT: B 306 GLN cc_start: 0.9060 (pp30) cc_final: 0.8667 (pm20) REVERT: B 375 ILE cc_start: 0.9813 (tp) cc_final: 0.9609 (pt) REVERT: C 121 GLN cc_start: 0.9771 (OUTLIER) cc_final: 0.9494 (pp30) REVERT: C 125 TYR cc_start: 0.9674 (m-80) cc_final: 0.8930 (t80) REVERT: C 155 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8869 (tppt) REVERT: C 253 ASP cc_start: 0.8910 (t0) cc_final: 0.8585 (t0) REVERT: D 7 MET cc_start: 0.8663 (tmm) cc_final: 0.8089 (tmm) REVERT: D 10 LYS cc_start: 0.9574 (mtpt) cc_final: 0.9168 (mtmm) REVERT: D 20 GLU cc_start: 0.8470 (tp30) cc_final: 0.8258 (tp30) REVERT: D 421 PHE cc_start: 0.9748 (m-80) cc_final: 0.9464 (t80) REVERT: D 439 HIS cc_start: 0.8987 (m90) cc_final: 0.8703 (m90) REVERT: E 52 MET cc_start: 0.9208 (mmm) cc_final: 0.8879 (mmt) REVERT: E 65 MET cc_start: 0.9076 (ppp) cc_final: 0.8290 (ppp) REVERT: E 71 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8821 (ptpt) REVERT: E 166 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7754 (pmm) REVERT: E 272 LEU cc_start: 0.9421 (mt) cc_final: 0.9116 (mp) REVERT: E 302 ASN cc_start: 0.9690 (t0) cc_final: 0.9470 (t0) REVERT: E 306 GLN cc_start: 0.8802 (pm20) cc_final: 0.8302 (pm20) REVERT: E 397 TYR cc_start: 0.9422 (m-80) cc_final: 0.9178 (m-80) REVERT: E 398 LYS cc_start: 0.9392 (ttpp) cc_final: 0.9147 (pttp) REVERT: E 418 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8046 (t) REVERT: F 117 MET cc_start: 0.9371 (mmm) cc_final: 0.8791 (mpp) REVERT: F 199 ARG cc_start: 0.8945 (ttp80) cc_final: 0.8709 (ttp80) REVERT: F 211 ASP cc_start: 0.9254 (t0) cc_final: 0.8813 (m-30) REVERT: F 217 LEU cc_start: 0.9771 (mm) cc_final: 0.9386 (tp) REVERT: F 236 ARG cc_start: 0.8742 (tpt170) cc_final: 0.8258 (pmt170) REVERT: G 136 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8343 (m) REVERT: G 386 ASP cc_start: 0.9510 (m-30) cc_final: 0.8800 (t0) REVERT: H 65 MET cc_start: 0.9183 (tmm) cc_final: 0.8722 (tmm) REVERT: H 167 HIS cc_start: 0.9556 (OUTLIER) cc_final: 0.9267 (p90) REVERT: I 178 TYR cc_start: 0.9671 (m-80) cc_final: 0.9208 (m-10) REVERT: I 223 MET cc_start: 0.1392 (ptm) cc_final: 0.0917 (ptt) REVERT: I 253 PHE cc_start: 0.8898 (m-10) cc_final: 0.8579 (m-10) REVERT: J 10 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9049 (mmtm) REVERT: J 45 GLU cc_start: 0.9431 (mm-30) cc_final: 0.8648 (tp30) REVERT: J 79 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.9003 (tp-100) REVERT: J 88 MET cc_start: 0.9363 (tpp) cc_final: 0.9019 (tpp) REVERT: J 197 LYS cc_start: 0.9587 (mmmt) cc_final: 0.9150 (mmmm) REVERT: J 418 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9082 (t) REVERT: K 52 MET cc_start: 0.8895 (mmm) cc_final: 0.8319 (mmm) REVERT: K 68 MET cc_start: 0.9093 (mmm) cc_final: 0.8706 (mmm) REVERT: K 171 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.8843 (pp) REVERT: K 302 ASN cc_start: 0.9623 (t0) cc_final: 0.9343 (t0) REVERT: L 107 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6233 (ptpp) REVERT: L 132 ARG cc_start: 0.9474 (tpp80) cc_final: 0.9122 (tpp80) REVERT: L 134 PHE cc_start: 0.9521 (m-80) cc_final: 0.8999 (m-80) REVERT: L 152 LYS cc_start: 0.9403 (tptt) cc_final: 0.9117 (tptt) REVERT: L 159 TYR cc_start: 0.9072 (m-10) cc_final: 0.8542 (m-10) REVERT: L 160 ASP cc_start: 0.9548 (t0) cc_final: 0.9195 (t0) REVERT: L 161 LEU cc_start: 0.9797 (OUTLIER) cc_final: 0.9461 (mm) REVERT: L 181 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6122 (mmtt) REVERT: L 217 LEU cc_start: 0.9386 (mm) cc_final: 0.8961 (tp) REVERT: L 239 LEU cc_start: 0.9402 (mm) cc_final: 0.9006 (mm) REVERT: L 241 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.9009 (p) REVERT: L 244 TRP cc_start: 0.9158 (m100) cc_final: 0.8416 (m-10) REVERT: L 252 LYS cc_start: 0.9511 (tppp) cc_final: 0.8700 (tptt) REVERT: M 6 MET cc_start: 0.9506 (tpp) cc_final: 0.9185 (tpp) REVERT: M 41 TYR cc_start: 0.9544 (t80) cc_final: 0.9060 (t80) REVERT: N 6 MET cc_start: 0.9625 (tpp) cc_final: 0.9407 (tpp) REVERT: N 36 MET cc_start: 0.9224 (ptm) cc_final: 0.8929 (ptp) REVERT: N 49 LEU cc_start: 0.9694 (tt) cc_final: 0.9281 (pp) REVERT: O 8 VAL cc_start: 0.9660 (OUTLIER) cc_final: 0.9412 (p) REVERT: O 9 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8155 (tt) REVERT: O 17 ASP cc_start: 0.9311 (p0) cc_final: 0.9084 (p0) REVERT: O 22 MET cc_start: 0.8619 (mmp) cc_final: 0.7965 (mmm) REVERT: O 36 MET cc_start: 0.8602 (tpt) cc_final: 0.8273 (tpp) REVERT: O 39 GLN cc_start: 0.9457 (mt0) cc_final: 0.9139 (pt0) REVERT: O 40 ASN cc_start: 0.9371 (m-40) cc_final: 0.8173 (m110) REVERT: P 9 LEU cc_start: 0.8161 (pp) cc_final: 0.7897 (pp) REVERT: P 22 MET cc_start: 0.9227 (tpt) cc_final: 0.8666 (mmm) REVERT: P 32 GLU cc_start: 0.9318 (pp20) cc_final: 0.9005 (pp20) REVERT: P 35 THR cc_start: 0.9619 (m) cc_final: 0.9220 (p) REVERT: P 36 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8850 (mmt) outliers start: 177 outliers final: 134 residues processed: 563 average time/residue: 0.4720 time to fit residues: 423.9033 Evaluate side-chains 560 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 400 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 204 LEU 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 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 418 THR Chi-restraints excluded: chain A residue 438 PHE 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 113 PHE 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 315 ASN Chi-restraints excluded: chain B residue 321 GLU 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 121 GLN 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 63 CYS Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 THR 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 289 THR Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 406 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 45 ILE 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 188 THR Chi-restraints excluded: chain E residue 270 GLU 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 178 THR Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 193 VAL 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 136 THR Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 192 GLU 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 329 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 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 251 LYS 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 384 TRP Chi-restraints excluded: chain I residue 257 ARG 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 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 272 CYS Chi-restraints excluded: chain J residue 274 VAL 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 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 123 ASN Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 181 LYS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 241 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 32 GLU Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 9 LEU 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 O residue 25 CYS 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 408 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 166 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 136 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** 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 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.091950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.082220 restraints weight = 241487.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.080872 restraints weight = 116177.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.081132 restraints weight = 83418.007| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 34264 Z= 0.238 Angle : 0.838 14.521 46758 Z= 0.412 Chirality : 0.049 0.417 5230 Planarity : 0.006 0.093 5982 Dihedral : 6.332 55.458 4865 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.44 % Rotamer: Outliers : 4.83 % Allowed : 30.39 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.12), residues: 4220 helix: -0.00 (0.22), residues: 520 sheet: -0.76 (0.16), residues: 1049 loop : -1.40 (0.12), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP R 50 HIS 0.013 0.001 HIS A 332 PHE 0.050 0.002 PHE G 421 TYR 0.022 0.002 TYR I 216 ARG 0.015 0.001 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 12) link_NAG-ASN : angle 3.59633 ( 36) hydrogen bonds : bond 0.03658 ( 1152) hydrogen bonds : angle 6.02332 ( 2994) SS BOND : bond 0.00415 ( 75) SS BOND : angle 1.59038 ( 150) covalent geometry : bond 0.00510 (34177) covalent geometry : angle 0.82906 (46572) *********************** 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 598 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 421 time to evaluate : 3.608 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 88 MET cc_start: 0.9547 (ppp) cc_final: 0.9107 (ppp) REVERT: A 204 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8255 (mt) REVERT: A 241 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: A 297 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8488 (p) REVERT: A 349 GLU cc_start: 0.9520 (OUTLIER) cc_final: 0.9298 (mm-30) REVERT: A 367 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.8861 (tptp) REVERT: A 385 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5923 (pptt) REVERT: B 113 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8943 (t80) REVERT: B 128 VAL cc_start: 0.9741 (OUTLIER) cc_final: 0.9530 (m) REVERT: B 274 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: B 280 LEU cc_start: 0.9827 (tp) cc_final: 0.9527 (pt) REVERT: B 306 GLN cc_start: 0.9058 (pp30) cc_final: 0.8658 (pm20) REVERT: C 125 TYR cc_start: 0.9698 (m-80) cc_final: 0.8971 (t80) REVERT: C 155 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8905 (tppt) REVERT: C 159 TYR cc_start: 0.9426 (m-10) cc_final: 0.9190 (m-10) REVERT: C 252 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8901 (mmtm) REVERT: C 253 ASP cc_start: 0.8862 (t0) cc_final: 0.8514 (t0) REVERT: D 7 MET cc_start: 0.8649 (tmm) cc_final: 0.8045 (tmm) REVERT: D 10 LYS cc_start: 0.9579 (mtpt) cc_final: 0.9170 (mtmm) REVERT: D 20 GLU cc_start: 0.8508 (tp30) cc_final: 0.8221 (tp30) REVERT: D 421 PHE cc_start: 0.9754 (m-80) cc_final: 0.9482 (t80) REVERT: D 439 HIS cc_start: 0.9073 (m90) cc_final: 0.8820 (m90) REVERT: E 52 MET cc_start: 0.9196 (mmm) cc_final: 0.8871 (mmt) REVERT: E 65 MET cc_start: 0.9074 (ppp) cc_final: 0.8279 (ppp) REVERT: E 71 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8861 (ptpt) REVERT: E 166 MET cc_start: 0.8201 (pmm) cc_final: 0.7827 (pmm) REVERT: E 302 ASN cc_start: 0.9675 (t0) cc_final: 0.9442 (t0) REVERT: E 306 GLN cc_start: 0.8855 (pm20) cc_final: 0.8352 (pm20) REVERT: E 321 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8842 (mp0) REVERT: E 379 CYS cc_start: 0.9777 (t) cc_final: 0.9510 (p) REVERT: E 397 TYR cc_start: 0.9477 (m-80) cc_final: 0.9236 (m-80) REVERT: E 398 LYS cc_start: 0.9394 (ttpp) cc_final: 0.9012 (pttp) REVERT: E 418 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8079 (t) REVERT: F 117 MET cc_start: 0.9506 (mmm) cc_final: 0.8996 (mpp) REVERT: F 199 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8562 (ttp80) REVERT: F 211 ASP cc_start: 0.9338 (t0) cc_final: 0.8872 (m-30) REVERT: F 217 LEU cc_start: 0.9783 (mm) cc_final: 0.9404 (tp) REVERT: G 132 MET cc_start: 0.9214 (tpp) cc_final: 0.8588 (tpp) REVERT: G 136 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8347 (m) REVERT: G 386 ASP cc_start: 0.9511 (m-30) cc_final: 0.8789 (t0) REVERT: H 65 MET cc_start: 0.9193 (tmm) cc_final: 0.8718 (tmm) REVERT: H 167 HIS cc_start: 0.9534 (OUTLIER) cc_final: 0.9242 (p90) REVERT: I 178 TYR cc_start: 0.9715 (m-80) cc_final: 0.9267 (m-10) REVERT: I 223 MET cc_start: 0.1907 (ptm) cc_final: 0.1350 (ptt) REVERT: I 253 PHE cc_start: 0.8958 (m-10) cc_final: 0.8553 (m-10) REVERT: I 292 LEU cc_start: 0.9534 (mm) cc_final: 0.9168 (mm) REVERT: J 10 LYS cc_start: 0.9321 (mmtm) cc_final: 0.9041 (mmtm) REVERT: J 45 GLU cc_start: 0.9419 (mm-30) cc_final: 0.8623 (tp30) REVERT: J 79 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.9019 (tp-100) REVERT: J 88 MET cc_start: 0.9389 (tpp) cc_final: 0.9026 (tpp) REVERT: J 197 LYS cc_start: 0.9584 (mmmt) cc_final: 0.9211 (mmmm) REVERT: J 418 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9099 (t) REVERT: K 52 MET cc_start: 0.8824 (mmm) cc_final: 0.8260 (mmm) REVERT: K 68 MET cc_start: 0.8995 (mmm) cc_final: 0.8630 (mmm) REVERT: K 171 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.8878 (pp) REVERT: K 302 ASN cc_start: 0.9624 (t0) cc_final: 0.9349 (t0) REVERT: L 107 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6376 (ptpp) REVERT: L 119 ASN cc_start: 0.9371 (t0) cc_final: 0.9081 (p0) REVERT: L 132 ARG cc_start: 0.9467 (tpp80) cc_final: 0.9137 (tpp80) REVERT: L 134 PHE cc_start: 0.9555 (m-80) cc_final: 0.9208 (m-80) REVERT: L 160 ASP cc_start: 0.9562 (t0) cc_final: 0.9288 (t0) REVERT: L 181 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6368 (mmtt) REVERT: L 217 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8974 (tp) REVERT: L 239 LEU cc_start: 0.9485 (mm) cc_final: 0.9124 (mm) REVERT: L 244 TRP cc_start: 0.9241 (OUTLIER) cc_final: 0.8564 (m-10) REVERT: M 6 MET cc_start: 0.9549 (tpp) cc_final: 0.9243 (tpp) REVERT: M 9 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9177 (mt) REVERT: M 41 TYR cc_start: 0.9529 (t80) cc_final: 0.9091 (t80) REVERT: M 49 LEU cc_start: 0.9560 (tt) cc_final: 0.9247 (pp) REVERT: N 6 MET cc_start: 0.9627 (tpp) cc_final: 0.9364 (tpp) REVERT: N 36 MET cc_start: 0.9253 (ptm) cc_final: 0.8979 (ptp) REVERT: N 49 LEU cc_start: 0.9674 (tt) cc_final: 0.9308 (pp) REVERT: O 8 VAL cc_start: 0.9596 (OUTLIER) cc_final: 0.9360 (p) REVERT: O 9 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7812 (tt) REVERT: O 22 MET cc_start: 0.8782 (mmp) cc_final: 0.8080 (mmm) REVERT: O 36 MET cc_start: 0.8630 (tpt) cc_final: 0.8282 (tpp) REVERT: O 39 GLN cc_start: 0.9438 (mt0) cc_final: 0.9139 (pt0) REVERT: O 40 ASN cc_start: 0.9359 (m-40) cc_final: 0.8164 (m110) REVERT: P 6 MET cc_start: 0.9215 (tpp) cc_final: 0.8629 (tpp) REVERT: P 9 LEU cc_start: 0.8230 (pp) cc_final: 0.8011 (pp) REVERT: P 32 GLU cc_start: 0.9355 (pp20) cc_final: 0.9045 (pp20) REVERT: P 35 THR cc_start: 0.9595 (m) cc_final: 0.9077 (p) REVERT: P 36 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.8805 (mmt) REVERT: P 39 GLN cc_start: 0.9570 (mm-40) cc_final: 0.9034 (pt0) outliers start: 177 outliers final: 138 residues processed: 567 average time/residue: 0.4678 time to fit residues: 424.4414 Evaluate side-chains 564 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 402 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 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 126 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 204 LEU 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 297 VAL 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 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 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 113 PHE 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 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 321 GLU 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 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 228 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 126 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 172 SER 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 303 LYS Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 406 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 45 ILE 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 177 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 270 GLU 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 185 PHE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 ILE 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 136 THR Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 192 GLU 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 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 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 H residue 384 TRP Chi-restraints excluded: chain I residue 257 ARG 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 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 203 ASP 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 329 CYS 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 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 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 137 LEU Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 181 LYS Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 244 TRP 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 32 GLU Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 11 ASN 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 O residue 25 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 287 optimal weight: 50.0000 chunk 216 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 408 optimal weight: 50.0000 chunk 1 optimal weight: 50.0000 chunk 367 optimal weight: 0.9990 chunk 409 optimal weight: 3.9990 chunk 329 optimal weight: 20.0000 chunk 227 optimal weight: 50.0000 chunk 286 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 120 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 ASN ** 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** ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.094278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.083673 restraints weight = 241744.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082447 restraints weight = 121339.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082748 restraints weight = 93514.175| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34264 Z= 0.163 Angle : 0.845 15.059 46758 Z= 0.412 Chirality : 0.049 0.409 5230 Planarity : 0.006 0.092 5982 Dihedral : 6.179 55.188 4865 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.65 % Rotamer: Outliers : 4.12 % Allowed : 31.01 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4220 helix: -0.03 (0.23), residues: 514 sheet: -0.68 (0.16), residues: 1082 loop : -1.40 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP R 50 HIS 0.014 0.001 HIS A 332 PHE 0.032 0.001 PHE G 95 TYR 0.025 0.001 TYR I 216 ARG 0.015 0.001 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 12) link_NAG-ASN : angle 3.58580 ( 36) hydrogen bonds : bond 0.03599 ( 1152) hydrogen bonds : angle 5.97083 ( 2994) SS BOND : bond 0.00309 ( 75) SS BOND : angle 1.42880 ( 150) covalent geometry : bond 0.00369 (34177) covalent geometry : angle 0.83693 (46572) ********************** 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 568 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 417 time to evaluate : 3.723 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: A 88 MET cc_start: 0.9579 (ppp) cc_final: 0.9080 (ppp) REVERT: A 161 LYS cc_start: 0.9750 (OUTLIER) cc_final: 0.9445 (tptm) REVERT: A 204 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8187 (mt) REVERT: A 241 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: A 297 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8436 (p) REVERT: A 349 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9295 (mm-30) REVERT: B 274 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8964 (pm20) REVERT: B 280 LEU cc_start: 0.9820 (tp) cc_final: 0.9578 (pt) REVERT: B 306 GLN cc_start: 0.9053 (pp30) cc_final: 0.8613 (pm20) REVERT: C 125 TYR cc_start: 0.9721 (m-80) cc_final: 0.9043 (t80) REVERT: C 159 TYR cc_start: 0.9437 (m-10) cc_final: 0.9163 (m-10) REVERT: C 252 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8958 (mmtm) REVERT: C 253 ASP cc_start: 0.8770 (t0) cc_final: 0.8472 (t0) REVERT: D 7 MET cc_start: 0.8642 (tmm) cc_final: 0.8073 (tmm) REVERT: D 10 LYS cc_start: 0.9559 (mtpt) cc_final: 0.9192 (mtmm) REVERT: D 20 GLU cc_start: 0.8432 (tp30) cc_final: 0.8122 (tp30) REVERT: D 421 PHE cc_start: 0.9769 (m-80) cc_final: 0.9506 (t80) REVERT: D 439 HIS cc_start: 0.9124 (m90) cc_final: 0.8848 (m90) REVERT: E 52 MET cc_start: 0.9190 (mmm) cc_final: 0.8883 (mmt) REVERT: E 65 MET cc_start: 0.9029 (ppp) cc_final: 0.8276 (ppp) REVERT: E 71 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8879 (ptpt) REVERT: E 166 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7769 (pmm) REVERT: E 302 ASN cc_start: 0.9684 (t0) cc_final: 0.9462 (t0) REVERT: E 306 GLN cc_start: 0.8797 (pm20) cc_final: 0.8293 (pm20) REVERT: E 321 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8884 (mp0) REVERT: E 379 CYS cc_start: 0.9765 (t) cc_final: 0.9506 (p) REVERT: E 397 TYR cc_start: 0.9519 (m-80) cc_final: 0.9283 (m-80) REVERT: E 398 LYS cc_start: 0.9436 (ttpp) cc_final: 0.9196 (pttp) REVERT: E 418 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (t) REVERT: F 117 MET cc_start: 0.9520 (mmm) cc_final: 0.8983 (mpp) REVERT: F 154 LYS cc_start: 0.9131 (pttm) cc_final: 0.8006 (pttm) REVERT: F 163 TYR cc_start: 0.9347 (p90) cc_final: 0.8637 (p90) REVERT: F 199 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8649 (ttp80) REVERT: F 211 ASP cc_start: 0.9378 (t0) cc_final: 0.8912 (m-30) REVERT: F 217 LEU cc_start: 0.9786 (mm) cc_final: 0.9440 (tp) REVERT: F 236 ARG cc_start: 0.8919 (tpt170) cc_final: 0.8424 (pmt170) REVERT: G 132 MET cc_start: 0.9177 (tpp) cc_final: 0.8630 (tpp) REVERT: G 136 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8277 (m) REVERT: G 188 TYR cc_start: 0.9222 (t80) cc_final: 0.8574 (t80) REVERT: G 386 ASP cc_start: 0.9504 (m-30) cc_final: 0.8807 (t0) REVERT: H 65 MET cc_start: 0.9157 (tmm) cc_final: 0.8686 (tmm) REVERT: H 167 HIS cc_start: 0.9500 (OUTLIER) cc_final: 0.9215 (p90) REVERT: I 178 TYR cc_start: 0.9744 (m-80) cc_final: 0.9345 (m-10) REVERT: I 223 MET cc_start: 0.1978 (ptm) cc_final: 0.1469 (ptt) REVERT: I 253 PHE cc_start: 0.9034 (m-10) cc_final: 0.8450 (m-10) REVERT: I 292 LEU cc_start: 0.9573 (mm) cc_final: 0.9219 (mm) REVERT: J 10 LYS cc_start: 0.9347 (mmtm) cc_final: 0.9049 (mmtm) REVERT: J 45 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8606 (tp30) REVERT: J 79 GLN cc_start: 0.9448 (OUTLIER) cc_final: 0.8939 (tm-30) REVERT: J 103 MET cc_start: 0.7824 (mmm) cc_final: 0.6703 (tpt) REVERT: J 197 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9131 (mmmm) REVERT: J 418 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9087 (t) REVERT: K 52 MET cc_start: 0.8844 (mmm) cc_final: 0.8258 (mmm) REVERT: K 68 MET cc_start: 0.8951 (mmm) cc_final: 0.8571 (mmm) REVERT: K 171 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.8897 (pp) REVERT: K 302 ASN cc_start: 0.9633 (t0) cc_final: 0.9275 (t0) REVERT: L 107 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6174 (ptpp) REVERT: L 119 ASN cc_start: 0.9417 (t0) cc_final: 0.9171 (p0) REVERT: L 132 ARG cc_start: 0.9467 (tpp80) cc_final: 0.9175 (tpp80) REVERT: L 134 PHE cc_start: 0.9591 (m-80) cc_final: 0.9282 (m-80) REVERT: L 160 ASP cc_start: 0.9545 (t0) cc_final: 0.9277 (t0) REVERT: L 181 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6566 (mmtt) REVERT: L 217 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9051 (tp) REVERT: L 239 LEU cc_start: 0.9536 (mm) cc_final: 0.9224 (mm) REVERT: L 244 TRP cc_start: 0.9304 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: M 6 MET cc_start: 0.9547 (tpp) cc_final: 0.9236 (tpp) REVERT: M 9 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9128 (mt) REVERT: M 41 TYR cc_start: 0.9487 (t80) cc_final: 0.9064 (t80) REVERT: M 49 LEU cc_start: 0.9528 (tt) cc_final: 0.9189 (pp) REVERT: N 6 MET cc_start: 0.9647 (tpp) cc_final: 0.9323 (tpp) REVERT: N 36 MET cc_start: 0.9215 (ptm) cc_final: 0.8933 (ptp) REVERT: N 49 LEU cc_start: 0.9606 (tt) cc_final: 0.9299 (pp) REVERT: O 8 VAL cc_start: 0.9559 (OUTLIER) cc_final: 0.9317 (p) REVERT: O 9 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7467 (tt) REVERT: O 22 MET cc_start: 0.8841 (mmp) cc_final: 0.8116 (mmm) REVERT: O 36 MET cc_start: 0.8657 (tpt) cc_final: 0.8314 (tpp) REVERT: O 39 GLN cc_start: 0.9345 (mt0) cc_final: 0.9071 (pt0) REVERT: O 40 ASN cc_start: 0.9337 (m-40) cc_final: 0.8048 (m110) REVERT: P 6 MET cc_start: 0.9176 (tpp) cc_final: 0.8571 (tpp) REVERT: P 9 LEU cc_start: 0.8325 (pp) cc_final: 0.8091 (pp) REVERT: P 32 GLU cc_start: 0.9360 (pp20) cc_final: 0.9076 (pp20) REVERT: P 35 THR cc_start: 0.9572 (m) cc_final: 0.9178 (p) REVERT: P 36 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8993 (mmt) REVERT: P 55 LYS cc_start: 0.9558 (tptp) cc_final: 0.9205 (pptt) outliers start: 151 outliers final: 113 residues processed: 537 average time/residue: 0.4867 time to fit residues: 420.3184 Evaluate side-chains 535 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 400 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 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 126 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 204 LEU 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 297 VAL 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 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 133 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 SER 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 304 THR Chi-restraints excluded: chain B residue 315 ASN Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 398 LYS 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 228 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 167 LEU Chi-restraints excluded: chain D residue 172 SER 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 60 VAL Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 270 GLU 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 185 PHE Chi-restraints excluded: chain F residue 193 VAL 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 260 CYS Chi-restraints excluded: chain G residue 272 CYS Chi-restraints excluded: chain G residue 289 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 424 LEU 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 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 H residue 384 TRP Chi-restraints excluded: chain I residue 219 VAL 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 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 274 VAL 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 44 VAL Chi-restraints excluded: chain K residue 93 SER 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 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 123 ASN Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 181 LYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 244 TRP 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 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 8 VAL Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 12 ILE Chi-restraints excluded: chain O residue 21 CYS Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain P residue 36 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 187 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 64 optimal weight: 50.0000 chunk 345 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 127 optimal weight: 30.0000 chunk 228 optimal weight: 50.0000 chunk 235 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 HIS ** E 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN L 123 ASN ** L 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.091764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.081491 restraints weight = 242248.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080363 restraints weight = 119717.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.080626 restraints weight = 88479.271| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 34264 Z= 0.225 Angle : 0.857 17.830 46758 Z= 0.420 Chirality : 0.049 0.410 5230 Planarity : 0.006 0.093 5982 Dihedral : 6.342 59.801 4865 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.56 % Favored : 92.39 % Rotamer: Outliers : 4.17 % Allowed : 31.01 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.03 % Twisted Proline : 0.34 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4220 helix: -0.02 (0.23), residues: 522 sheet: -0.69 (0.16), residues: 1064 loop : -1.39 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.002 TRP R 50 HIS 0.013 0.001 HIS A 332 PHE 0.046 0.002 PHE G 421 TYR 0.028 0.002 TYR L 125 ARG 0.015 0.001 ARG E 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00693 ( 12) link_NAG-ASN : angle 4.66150 ( 36) hydrogen bonds : bond 0.03679 ( 1152) hydrogen bonds : angle 6.02606 ( 2994) SS BOND : bond 0.00390 ( 75) SS BOND : angle 1.54246 ( 150) covalent geometry : bond 0.00487 (34177) covalent geometry : angle 0.84405 (46572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12778.38 seconds wall clock time: 223 minutes 18.65 seconds (13398.65 seconds total)