Starting phenix.real_space_refine on Thu Mar 5 05:32:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyq_34376/03_2026/8gyq_34376.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyq_34376/03_2026/8gyq_34376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gyq_34376/03_2026/8gyq_34376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyq_34376/03_2026/8gyq_34376.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyq_34376/03_2026/8gyq_34376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyq_34376/03_2026/8gyq_34376.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 12726 2.51 5 N 3402 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "E" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "G" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "F" 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 Time building chain proxies: 4.52, per 1000 atoms: 0.23 Number of scatterers: 19712 At special positions: 0 Unit cell: (125.19, 125.19, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 3493 8.00 N 3402 7.00 C 12726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 279 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 279 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 279 " distance=2.03 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 259 " distance=2.03 Simple disulfide: pdb=" SG CYS G 81 " - pdb=" SG CYS G 279 " distance=2.03 Simple disulfide: pdb=" SG CYS G 99 " - pdb=" SG CYS G 259 " distance=2.03 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 701 " - " ASN A 86 " " NAG B 701 " - " ASN B 86 " " NAG C 701 " - " ASN C 86 " " NAG D 701 " - " ASN D 86 " " NAG E 701 " - " ASN E 86 " " NAG F 701 " - " ASN F 86 " " NAG G 701 " - " ASN G 86 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 820.7 milliseconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 75.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 48 through 76 removed outlier: 3.815A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.767A pdb=" N TRP A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 183 removed outlier: 4.011A pdb=" N LYS A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.291A pdb=" N LEU A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Proline residue: A 138 - end of helix removed outlier: 5.472A pdb=" N THR A 148 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 174 - end of helix removed outlier: 4.004A pdb=" N GLU A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.827A pdb=" N ARG A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 251 removed outlier: 3.836A pdb=" N VAL A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix removed outlier: 3.759A pdb=" N THR A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 314 removed outlier: 3.624A pdb=" N GLY A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 removed outlier: 3.783A pdb=" N VAL A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.589A pdb=" N TRP A 336 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.675A pdb=" N ILE A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 367 removed outlier: 3.897A pdb=" N ASN A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 4.262A pdb=" N ASP A 376 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.699A pdb=" N ALA A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 76 removed outlier: 3.502A pdb=" N ARG B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Proline residue: B 62 - end of helix Processing helix chain 'B' and resid 88 through 103 removed outlier: 3.900A pdb=" N TRP B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 183 removed outlier: 3.932A pdb=" N LYS B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 4.404A pdb=" N LEU B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Proline residue: B 138 - end of helix removed outlier: 5.691A pdb=" N THR B 148 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Proline residue: B 174 - end of helix removed outlier: 4.023A pdb=" N GLU B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.928A pdb=" N ARG B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 251 removed outlier: 3.871A pdb=" N VAL B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 283 through 314 Processing helix chain 'B' and resid 319 through 329 removed outlier: 3.911A pdb=" N VAL B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.615A pdb=" N TRP B 336 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.634A pdb=" N ILE B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.919A pdb=" N ASN B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 376 removed outlier: 3.891A pdb=" N ASP B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.976A pdb=" N ALA B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 76 removed outlier: 3.862A pdb=" N ARG C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.943A pdb=" N TRP C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 183 removed outlier: 3.998A pdb=" N LYS C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Proline residue: C 125 - end of helix removed outlier: 4.349A pdb=" N LEU C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 5.666A pdb=" N THR C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Proline residue: C 174 - end of helix removed outlier: 4.048A pdb=" N GLU C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 251 removed outlier: 3.836A pdb=" N VAL C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Proline residue: C 241 - end of helix Processing helix chain 'C' and resid 283 through 314 removed outlier: 3.523A pdb=" N GLY C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.752A pdb=" N VAL C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.593A pdb=" N TRP C 336 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.929A pdb=" N ILE C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 358 through 367 removed outlier: 3.916A pdb=" N ASN C 362 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 removed outlier: 3.725A pdb=" N ASP C 376 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.710A pdb=" N ALA C 384 " --> pdb=" O ARG C 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 76 removed outlier: 3.789A pdb=" N ARG D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Proline residue: D 62 - end of helix Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.888A pdb=" N TRP D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 183 removed outlier: 3.992A pdb=" N LYS D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Proline residue: D 125 - end of helix removed outlier: 4.316A pdb=" N LEU D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 5.734A pdb=" N THR D 148 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 159 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Proline residue: D 174 - end of helix removed outlier: 4.059A pdb=" N GLU D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG D 219 " --> pdb=" O GLU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 251 removed outlier: 3.848A pdb=" N VAL D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Proline residue: D 241 - end of helix removed outlier: 3.784A pdb=" N THR D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 314 removed outlier: 3.572A pdb=" N GLY D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 329 removed outlier: 3.762A pdb=" N VAL D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.563A pdb=" N TRP D 336 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 removed outlier: 3.907A pdb=" N ILE D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 358 through 367 removed outlier: 3.801A pdb=" N ASN D 362 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 376 removed outlier: 4.019A pdb=" N ASP D 376 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 389 removed outlier: 3.717A pdb=" N ALA D 384 " --> pdb=" O ARG D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 76 removed outlier: 5.107A pdb=" N VAL E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.812A pdb=" N TRP E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 183 removed outlier: 4.001A pdb=" N LYS E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Proline residue: E 125 - end of helix removed outlier: 4.308A pdb=" N LEU E 129 " --> pdb=" O PRO E 125 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 5.663A pdb=" N THR E 148 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) Proline residue: E 174 - end of helix removed outlier: 4.030A pdb=" N GLU E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 202 Processing helix chain 'E' and resid 204 through 219 removed outlier: 3.843A pdb=" N ARG E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 251 removed outlier: 3.842A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Proline residue: E 241 - end of helix removed outlier: 3.566A pdb=" N THR E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 314 removed outlier: 3.602A pdb=" N GLY E 292 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 329 removed outlier: 3.767A pdb=" N VAL E 328 " --> pdb=" O LYS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 removed outlier: 3.582A pdb=" N TRP E 336 " --> pdb=" O ARG E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 354 removed outlier: 3.864A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 357 No H-bonds generated for 'chain 'E' and resid 355 through 357' Processing helix chain 'E' and resid 358 through 367 removed outlier: 3.888A pdb=" N ASN E 362 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG E 363 " --> pdb=" O LYS E 359 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE E 366 " --> pdb=" O ASN E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.954A pdb=" N ASP E 376 " --> pdb=" O LEU E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.730A pdb=" N ALA E 384 " --> pdb=" O ARG E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 76 removed outlier: 5.112A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Proline residue: F 62 - end of helix Processing helix chain 'F' and resid 88 through 102 removed outlier: 3.828A pdb=" N TRP F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 183 removed outlier: 4.028A pdb=" N LYS F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Proline residue: F 125 - end of helix removed outlier: 4.377A pdb=" N LEU F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Proline residue: F 138 - end of helix removed outlier: 5.491A pdb=" N THR F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN F 159 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA F 173 " --> pdb=" O ALA F 169 " (cutoff:3.500A) Proline residue: F 174 - end of helix removed outlier: 4.015A pdb=" N GLU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 202 Processing helix chain 'F' and resid 204 through 219 removed outlier: 3.816A pdb=" N ARG F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 251 removed outlier: 3.843A pdb=" N VAL F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Proline residue: F 241 - end of helix removed outlier: 3.746A pdb=" N THR F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 314 removed outlier: 3.641A pdb=" N GLY F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 329 removed outlier: 3.783A pdb=" N VAL F 328 " --> pdb=" O LYS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 removed outlier: 3.590A pdb=" N TRP F 336 " --> pdb=" O ARG F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 354 removed outlier: 3.794A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 357 No H-bonds generated for 'chain 'F' and resid 355 through 357' Processing helix chain 'F' and resid 358 through 367 removed outlier: 4.045A pdb=" N ASN F 362 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 376 removed outlier: 4.190A pdb=" N ASP F 376 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.682A pdb=" N ALA F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 76 removed outlier: 5.109A pdb=" N VAL G 61 " --> pdb=" O GLY G 57 " (cutoff:3.500A) Proline residue: G 62 - end of helix Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.810A pdb=" N TRP G 100 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 183 removed outlier: 3.964A pdb=" N LYS G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Proline residue: G 125 - end of helix removed outlier: 4.283A pdb=" N LEU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Proline residue: G 138 - end of helix removed outlier: 5.496A pdb=" N THR G 148 " --> pdb=" O PHE G 144 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ARG G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN G 159 " --> pdb=" O ASN G 155 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) Proline residue: G 174 - end of helix removed outlier: 4.001A pdb=" N GLU G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 202 Processing helix chain 'G' and resid 204 through 219 removed outlier: 3.846A pdb=" N ARG G 219 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 251 removed outlier: 3.854A pdb=" N VAL G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) Proline residue: G 241 - end of helix Processing helix chain 'G' and resid 283 through 314 removed outlier: 3.578A pdb=" N GLY G 292 " --> pdb=" O ARG G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 329 removed outlier: 3.784A pdb=" N VAL G 328 " --> pdb=" O LYS G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 removed outlier: 3.594A pdb=" N TRP G 336 " --> pdb=" O ARG G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 354 removed outlier: 3.990A pdb=" N ILE G 346 " --> pdb=" O CYS G 342 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 358 through 367 removed outlier: 3.958A pdb=" N ASN G 362 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG G 363 " --> pdb=" O LYS G 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 366 " --> pdb=" O ASN G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 376 removed outlier: 4.260A pdb=" N ASP G 376 " --> pdb=" O LEU G 373 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 389 removed outlier: 3.691A pdb=" N ALA G 384 " --> pdb=" O ARG G 380 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 1244 hydrogen bonds defined for protein. 3669 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: 2.88 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6310 1.34 - 1.46: 2516 1.46 - 1.57: 11186 1.57 - 1.69: 1 1.69 - 1.81: 119 Bond restraints: 20132 Sorted by residual: bond pdb=" CG PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 1.503 1.416 0.087 3.40e-02 8.65e+02 6.48e+00 bond pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.10e+00 bond pdb=" N LEU D 48 " pdb=" CA LEU D 48 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.41e-02 5.03e+03 5.00e+00 bond pdb=" CB PRO C 49 " pdb=" CG PRO C 49 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" C PRO A 49 " pdb=" O PRO A 49 " ideal model delta sigma weight residual 1.235 1.218 0.017 1.30e-02 5.92e+03 1.69e+00 ... (remaining 20127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26746 1.79 - 3.58: 456 3.58 - 5.37: 60 5.37 - 7.16: 4 7.16 - 8.95: 6 Bond angle restraints: 27272 Sorted by residual: angle pdb=" CA PRO C 49 " pdb=" N PRO C 49 " pdb=" CD PRO C 49 " ideal model delta sigma weight residual 112.00 103.61 8.39 1.40e+00 5.10e-01 3.59e+01 angle pdb=" N PRO C 49 " pdb=" CD PRO C 49 " pdb=" CG PRO C 49 " ideal model delta sigma weight residual 103.20 96.31 6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" CB LYS A 203 " pdb=" CG LYS A 203 " pdb=" CD LYS A 203 " ideal model delta sigma weight residual 111.30 120.25 -8.95 2.30e+00 1.89e-01 1.51e+01 angle pdb=" CB LYS F 203 " pdb=" CG LYS F 203 " pdb=" CD LYS F 203 " ideal model delta sigma weight residual 111.30 118.99 -7.69 2.30e+00 1.89e-01 1.12e+01 angle pdb=" CB LYS C 203 " pdb=" CG LYS C 203 " pdb=" CD LYS C 203 " ideal model delta sigma weight residual 111.30 118.69 -7.39 2.30e+00 1.89e-01 1.03e+01 ... (remaining 27267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 10459 17.93 - 35.87: 1345 35.87 - 53.80: 430 53.80 - 71.73: 57 71.73 - 89.67: 22 Dihedral angle restraints: 12313 sinusoidal: 5138 harmonic: 7175 Sorted by residual: dihedral pdb=" CA VAL A 378 " pdb=" C VAL A 378 " pdb=" N VAL A 379 " pdb=" CA VAL A 379 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA VAL G 378 " pdb=" C VAL G 378 " pdb=" N VAL G 379 " pdb=" CA VAL G 379 " ideal model delta harmonic sigma weight residual -180.00 -157.05 -22.95 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA VAL D 378 " pdb=" C VAL D 378 " pdb=" N VAL D 379 " pdb=" CA VAL D 379 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 12310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2228 0.033 - 0.067: 660 0.067 - 0.100: 174 0.100 - 0.133: 58 0.133 - 0.167: 2 Chirality restraints: 3122 Sorted by residual: chirality pdb=" CA LEU A 48 " pdb=" N LEU A 48 " pdb=" C LEU A 48 " pdb=" CB LEU A 48 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA LEU D 48 " pdb=" N LEU D 48 " pdb=" C LEU D 48 " pdb=" CB LEU D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA PRO B 49 " pdb=" N PRO B 49 " pdb=" C PRO B 49 " pdb=" CB PRO B 49 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 3119 not shown) Planarity restraints: 3465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 86 " -0.167 2.00e-02 2.50e+03 3.18e-01 1.27e+03 pdb=" CG ASN C 86 " 0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN C 86 " -0.121 2.00e-02 2.50e+03 pdb=" ND2 ASN C 86 " 0.565 2.00e-02 2.50e+03 pdb=" C1 NAG C 701 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 86 " -0.189 2.00e-02 2.50e+03 2.25e-01 6.34e+02 pdb=" CG ASN B 86 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN B 86 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 86 " 0.374 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.269 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 86 " 0.083 2.00e-02 2.50e+03 1.61e-01 3.23e+02 pdb=" CG ASN G 86 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN G 86 " 0.074 2.00e-02 2.50e+03 pdb=" ND2 ASN G 86 " -0.289 2.00e-02 2.50e+03 pdb=" C1 NAG G 701 " 0.176 2.00e-02 2.50e+03 ... (remaining 3462 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 114 2.45 - 3.06: 14039 3.06 - 3.68: 30523 3.68 - 4.29: 41389 4.29 - 4.90: 69771 Nonbonded interactions: 155836 Sorted by model distance: nonbonded pdb=" OD2 ASP C 51 " pdb=" OH TYR C 227 " model vdw 1.840 3.040 nonbonded pdb=" OG1 THR D 88 " pdb=" OD1 ASP D 90 " model vdw 1.903 3.040 nonbonded pdb=" OD2 ASP A 51 " pdb=" OH TYR A 227 " model vdw 1.914 3.040 nonbonded pdb=" OG1 THR B 88 " pdb=" OD1 ASP B 90 " model vdw 1.956 3.040 nonbonded pdb=" OD2 ASP F 51 " pdb=" OH TYR F 227 " model vdw 2.003 3.040 ... (remaining 155831 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 16.930 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.003 0.087 20153 Z= 0.145 Angle : 0.779 54.732 27321 Z= 0.351 Chirality : 0.035 0.167 3122 Planarity : 0.005 0.149 3458 Dihedral : 17.626 89.668 7595 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.27 % Favored : 92.56 % Rotamer: Outliers : 0.66 % Allowed : 26.32 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2394 helix: 1.49 (0.13), residues: 1540 sheet: -1.76 (0.60), residues: 105 loop : -2.51 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 167 TYR 0.013 0.001 TYR B 249 PHE 0.019 0.001 PHE A 50 TRP 0.008 0.001 TRP D 115 HIS 0.002 0.000 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00293 (20132) covalent geometry : angle 0.58089 (27272) SS BOND : bond 0.00247 ( 14) SS BOND : angle 0.42481 ( 28) hydrogen bonds : bond 0.10313 ( 1244) hydrogen bonds : angle 5.46858 ( 3669) link_NAG-ASN : bond 0.06834 ( 7) link_NAG-ASN : angle 18.76226 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 HIS cc_start: 0.8494 (t70) cc_final: 0.7907 (t-170) REVERT: A 380 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7102 (mtt180) REVERT: C 160 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5878 (tt0) REVERT: C 342 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7970 (p) REVERT: D 326 HIS cc_start: 0.8307 (t70) cc_final: 0.7925 (t70) REVERT: D 342 CYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8148 (p) REVERT: D 350 PHE cc_start: 0.7413 (m-80) cc_final: 0.7158 (m-80) REVERT: E 160 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5690 (tt0) REVERT: E 326 HIS cc_start: 0.8445 (t70) cc_final: 0.8064 (t-170) REVERT: E 342 CYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7516 (p) REVERT: F 160 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5471 (tt0) REVERT: G 160 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.5311 (tt0) REVERT: G 326 HIS cc_start: 0.8652 (t70) cc_final: 0.8036 (t-170) REVERT: G 342 CYS cc_start: 0.8394 (t) cc_final: 0.7833 (p) REVERT: G 380 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6955 (mtt90) outliers start: 14 outliers final: 4 residues processed: 270 average time/residue: 0.1257 time to fit residues: 55.1686 Evaluate side-chains 239 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 365 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN A 319 ASN B 163 ASN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS C 121 HIS C 319 ASN D 252 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN E 254 GLN E 319 ASN F 207 GLN F 319 ASN G 85 HIS G 254 GLN G 319 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.191546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125625 restraints weight = 27161.077| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.80 r_work: 0.3529 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20153 Z= 0.203 Angle : 0.726 17.546 27321 Z= 0.351 Chirality : 0.045 0.717 3122 Planarity : 0.005 0.085 3458 Dihedral : 7.266 71.521 2830 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 6.30 % Allowed : 23.68 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2394 helix: 1.26 (0.13), residues: 1610 sheet: -1.79 (0.60), residues: 105 loop : -2.58 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 167 TYR 0.013 0.002 TYR B 165 PHE 0.022 0.002 PHE A 350 TRP 0.015 0.002 TRP G 115 HIS 0.003 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00494 (20132) covalent geometry : angle 0.69271 (27272) SS BOND : bond 0.00668 ( 14) SS BOND : angle 0.57484 ( 28) hydrogen bonds : bond 0.03999 ( 1244) hydrogen bonds : angle 4.53292 ( 3669) link_NAG-ASN : bond 0.01080 ( 7) link_NAG-ASN : angle 7.86748 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 243 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4460 (OUTLIER) cc_final: 0.3736 (tt0) REVERT: A 210 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6019 (m-80) REVERT: A 326 HIS cc_start: 0.8221 (t70) cc_final: 0.7696 (t-170) REVERT: B 51 ASP cc_start: 0.7388 (m-30) cc_final: 0.7118 (m-30) REVERT: B 252 GLN cc_start: 0.8239 (tp40) cc_final: 0.7867 (tp40) REVERT: C 160 GLU cc_start: 0.4964 (OUTLIER) cc_final: 0.4685 (tt0) REVERT: C 210 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: D 210 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: D 326 HIS cc_start: 0.7939 (t70) cc_final: 0.7698 (t70) REVERT: D 350 PHE cc_start: 0.7596 (m-80) cc_final: 0.7096 (m-80) REVERT: E 160 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.5016 (tt0) REVERT: E 207 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6702 (tt0) REVERT: E 210 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: E 326 HIS cc_start: 0.8184 (t70) cc_final: 0.7809 (t-170) REVERT: F 160 GLU cc_start: 0.4906 (OUTLIER) cc_final: 0.4044 (tt0) REVERT: F 210 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: G 160 GLU cc_start: 0.5008 (OUTLIER) cc_final: 0.4287 (tt0) REVERT: G 210 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6433 (m-80) REVERT: G 326 HIS cc_start: 0.8354 (t70) cc_final: 0.7834 (t-170) REVERT: G 342 CYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7801 (p) REVERT: G 350 PHE cc_start: 0.7532 (m-80) cc_final: 0.7214 (m-80) outliers start: 134 outliers final: 89 residues processed: 329 average time/residue: 0.1095 time to fit residues: 59.1554 Evaluate side-chains 309 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 207 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 207 GLN Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 91 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 377 ASN C 319 ASN D 91 GLN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 ASN E 319 ASN F 91 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.191408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125423 restraints weight = 27344.874| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.79 r_work: 0.3532 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20153 Z= 0.183 Angle : 0.686 15.718 27321 Z= 0.334 Chirality : 0.044 0.632 3122 Planarity : 0.005 0.073 3458 Dihedral : 7.030 70.177 2823 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 7.00 % Allowed : 24.11 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 2394 helix: 1.32 (0.13), residues: 1638 sheet: -1.73 (0.59), residues: 105 loop : -2.52 (0.27), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 104 TYR 0.020 0.002 TYR B 213 PHE 0.025 0.001 PHE F 350 TRP 0.017 0.002 TRP B 115 HIS 0.007 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00445 (20132) covalent geometry : angle 0.65790 (27272) SS BOND : bond 0.00572 ( 14) SS BOND : angle 0.59643 ( 28) hydrogen bonds : bond 0.03807 ( 1244) hydrogen bonds : angle 4.41553 ( 3669) link_NAG-ASN : bond 0.01022 ( 7) link_NAG-ASN : angle 7.04008 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 216 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4570 (OUTLIER) cc_final: 0.3848 (tt0) REVERT: A 210 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6074 (m-80) REVERT: A 326 HIS cc_start: 0.8366 (t70) cc_final: 0.7829 (t-170) REVERT: B 51 ASP cc_start: 0.7476 (m-30) cc_final: 0.7174 (m-30) REVERT: B 191 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6782 (tp30) REVERT: B 334 ARG cc_start: 0.7502 (ptp90) cc_final: 0.7248 (ttp80) REVERT: B 377 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6702 (m-40) REVERT: C 160 GLU cc_start: 0.5189 (OUTLIER) cc_final: 0.4927 (tt0) REVERT: C 210 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: C 380 ARG cc_start: 0.6384 (mtt90) cc_final: 0.6057 (mtm180) REVERT: D 210 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: D 350 PHE cc_start: 0.7648 (m-80) cc_final: 0.7174 (m-80) REVERT: E 160 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.5152 (tt0) REVERT: E 210 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: E 326 HIS cc_start: 0.8232 (t70) cc_final: 0.7831 (t-170) REVERT: F 160 GLU cc_start: 0.5065 (OUTLIER) cc_final: 0.4328 (tt0) REVERT: F 210 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: F 380 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7374 (mtt90) REVERT: G 42 LEU cc_start: 0.1099 (OUTLIER) cc_final: 0.0833 (pp) REVERT: G 160 GLU cc_start: 0.5076 (OUTLIER) cc_final: 0.4360 (tt0) REVERT: G 210 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: G 326 HIS cc_start: 0.8347 (t70) cc_final: 0.7836 (t-170) REVERT: G 342 CYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7794 (p) REVERT: G 350 PHE cc_start: 0.7545 (m-80) cc_final: 0.7198 (m-80) outliers start: 149 outliers final: 113 residues processed: 322 average time/residue: 0.1187 time to fit residues: 62.5967 Evaluate side-chains 330 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 202 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 373 LEU Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 25 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 149 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 163 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 HIS F 207 GLN F 319 ASN F 377 ASN G 319 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.193316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125582 restraints weight = 27440.275| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.96 r_work: 0.3516 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20153 Z= 0.176 Angle : 0.666 14.000 27321 Z= 0.326 Chirality : 0.043 0.579 3122 Planarity : 0.005 0.070 3458 Dihedral : 6.864 66.686 2823 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 7.94 % Allowed : 23.68 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2394 helix: 1.45 (0.13), residues: 1624 sheet: -1.71 (0.58), residues: 105 loop : -2.50 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 380 TYR 0.019 0.002 TYR B 165 PHE 0.037 0.001 PHE E 350 TRP 0.019 0.002 TRP B 115 HIS 0.007 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00429 (20132) covalent geometry : angle 0.64340 (27272) SS BOND : bond 0.00552 ( 14) SS BOND : angle 0.60473 ( 28) hydrogen bonds : bond 0.03682 ( 1244) hydrogen bonds : angle 4.35215 ( 3669) link_NAG-ASN : bond 0.00905 ( 7) link_NAG-ASN : angle 6.21826 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 230 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4532 (OUTLIER) cc_final: 0.3820 (tt0) REVERT: A 210 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6148 (m-80) REVERT: A 326 HIS cc_start: 0.8364 (t70) cc_final: 0.8153 (t70) REVERT: A 380 ARG cc_start: 0.7754 (mtt180) cc_final: 0.7140 (mtt90) REVERT: B 51 ASP cc_start: 0.7623 (m-30) cc_final: 0.7304 (m-30) REVERT: B 191 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6898 (tp30) REVERT: B 334 ARG cc_start: 0.7525 (ptp90) cc_final: 0.7232 (ttp80) REVERT: C 160 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.5168 (tt0) REVERT: C 191 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8013 (tm-30) REVERT: C 210 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: D 210 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: D 350 PHE cc_start: 0.7594 (m-80) cc_final: 0.7123 (m-80) REVERT: E 160 GLU cc_start: 0.5519 (OUTLIER) cc_final: 0.5131 (tt0) REVERT: E 210 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: E 326 HIS cc_start: 0.8208 (t70) cc_final: 0.7827 (t-170) REVERT: E 380 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7051 (mtm180) REVERT: F 160 GLU cc_start: 0.5038 (OUTLIER) cc_final: 0.4314 (tt0) REVERT: F 210 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6301 (m-80) REVERT: F 380 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7738 (mtt90) REVERT: G 42 LEU cc_start: 0.1079 (OUTLIER) cc_final: 0.0833 (pp) REVERT: G 160 GLU cc_start: 0.5045 (OUTLIER) cc_final: 0.4335 (tt0) REVERT: G 210 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: G 326 HIS cc_start: 0.8338 (t70) cc_final: 0.7956 (t-170) REVERT: G 350 PHE cc_start: 0.7588 (m-80) cc_final: 0.7340 (m-80) REVERT: G 380 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7555 (mtm180) outliers start: 169 outliers final: 123 residues processed: 357 average time/residue: 0.1152 time to fit residues: 67.1570 Evaluate side-chains 341 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 205 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 93 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 71 optimal weight: 0.0040 chunk 185 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 198 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.196377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128068 restraints weight = 27078.800| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.04 r_work: 0.3557 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20153 Z= 0.126 Angle : 0.635 12.868 27321 Z= 0.310 Chirality : 0.041 0.518 3122 Planarity : 0.005 0.065 3458 Dihedral : 6.467 59.883 2821 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.59 % Allowed : 26.74 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2394 helix: 1.65 (0.13), residues: 1631 sheet: -1.46 (0.57), residues: 105 loop : -2.50 (0.26), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 167 TYR 0.014 0.001 TYR B 165 PHE 0.020 0.001 PHE A 350 TRP 0.014 0.001 TRP B 115 HIS 0.007 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00283 (20132) covalent geometry : angle 0.61467 (27272) SS BOND : bond 0.00259 ( 14) SS BOND : angle 0.61009 ( 28) hydrogen bonds : bond 0.03369 ( 1244) hydrogen bonds : angle 4.20452 ( 3669) link_NAG-ASN : bond 0.00821 ( 7) link_NAG-ASN : angle 5.71917 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 231 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.3739 (tt0) REVERT: A 210 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6093 (m-80) REVERT: A 326 HIS cc_start: 0.8369 (t70) cc_final: 0.8148 (t70) REVERT: A 380 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7499 (mtm180) REVERT: B 51 ASP cc_start: 0.7662 (m-30) cc_final: 0.7348 (m-30) REVERT: B 191 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7037 (tp30) REVERT: B 334 ARG cc_start: 0.7588 (ptp90) cc_final: 0.7306 (ttp80) REVERT: B 359 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5979 (mppt) REVERT: C 70 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8699 (m-10) REVERT: C 120 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7780 (pt0) REVERT: C 160 GLU cc_start: 0.5477 (OUTLIER) cc_final: 0.5271 (tt0) REVERT: C 191 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7964 (tm-30) REVERT: C 210 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: C 380 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7349 (mtm180) REVERT: D 210 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: D 350 PHE cc_start: 0.7555 (m-80) cc_final: 0.7118 (m-80) REVERT: E 160 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4971 (tt0) REVERT: E 210 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6908 (m-80) REVERT: E 326 HIS cc_start: 0.8193 (t70) cc_final: 0.7826 (t-170) REVERT: E 380 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7262 (mtm180) REVERT: F 150 LEU cc_start: 0.6992 (tp) cc_final: 0.6751 (tp) REVERT: F 160 GLU cc_start: 0.5297 (OUTLIER) cc_final: 0.4492 (tt0) REVERT: F 210 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: F 380 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7740 (mtt90) REVERT: G 42 LEU cc_start: 0.1114 (OUTLIER) cc_final: 0.0890 (pp) REVERT: G 160 GLU cc_start: 0.5025 (OUTLIER) cc_final: 0.4337 (tt0) REVERT: G 210 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: G 326 HIS cc_start: 0.8348 (t70) cc_final: 0.7978 (t-170) REVERT: G 342 CYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7847 (p) REVERT: G 350 PHE cc_start: 0.7585 (m-80) cc_final: 0.7366 (m-80) REVERT: G 380 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7250 (mtm180) outliers start: 119 outliers final: 78 residues processed: 326 average time/residue: 0.1235 time to fit residues: 64.7103 Evaluate side-chains 298 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 204 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 6 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 219 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN C 207 GLN C 362 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 ASN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.196713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128452 restraints weight = 27028.913| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.05 r_work: 0.3564 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20153 Z= 0.127 Angle : 0.623 11.899 27321 Z= 0.305 Chirality : 0.040 0.479 3122 Planarity : 0.005 0.065 3458 Dihedral : 6.104 57.112 2819 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.06 % Allowed : 27.07 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 2394 helix: 1.75 (0.13), residues: 1638 sheet: -1.30 (0.57), residues: 105 loop : -2.58 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 380 TYR 0.013 0.001 TYR B 165 PHE 0.018 0.001 PHE A 350 TRP 0.014 0.001 TRP B 115 HIS 0.003 0.000 HIS F 311 Details of bonding type rmsd covalent geometry : bond 0.00287 (20132) covalent geometry : angle 0.60402 (27272) SS BOND : bond 0.00279 ( 14) SS BOND : angle 0.53327 ( 28) hydrogen bonds : bond 0.03261 ( 1244) hydrogen bonds : angle 4.13242 ( 3669) link_NAG-ASN : bond 0.00832 ( 7) link_NAG-ASN : angle 5.51878 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 233 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4542 (OUTLIER) cc_final: 0.3894 (tt0) REVERT: A 210 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6024 (m-80) REVERT: A 326 HIS cc_start: 0.8355 (t70) cc_final: 0.8131 (t70) REVERT: A 332 THR cc_start: 0.4841 (OUTLIER) cc_final: 0.4545 (p) REVERT: B 51 ASP cc_start: 0.7637 (m-30) cc_final: 0.7319 (m-30) REVERT: B 334 ARG cc_start: 0.7587 (ptp90) cc_final: 0.7310 (ttp80) REVERT: B 359 LYS cc_start: 0.6396 (OUTLIER) cc_final: 0.6139 (mppt) REVERT: C 70 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8689 (m-10) REVERT: C 380 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7454 (mtm180) REVERT: D 135 MET cc_start: 0.8812 (tpp) cc_final: 0.8557 (mmm) REVERT: D 210 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7152 (m-80) REVERT: D 350 PHE cc_start: 0.7496 (m-80) cc_final: 0.7056 (m-80) REVERT: D 380 ARG cc_start: 0.6975 (mtt90) cc_final: 0.6231 (mtm180) REVERT: E 160 GLU cc_start: 0.5293 (OUTLIER) cc_final: 0.4851 (tt0) REVERT: E 210 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: E 326 HIS cc_start: 0.8213 (t70) cc_final: 0.7841 (t-170) REVERT: E 342 CYS cc_start: 0.8583 (t) cc_final: 0.7556 (p) REVERT: E 380 ARG cc_start: 0.7750 (mtt180) cc_final: 0.7243 (mtm180) REVERT: F 160 GLU cc_start: 0.5210 (OUTLIER) cc_final: 0.4493 (tt0) REVERT: F 210 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.6280 (m-80) REVERT: F 380 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7767 (mtt90) REVERT: G 42 LEU cc_start: 0.1109 (OUTLIER) cc_final: 0.0885 (pp) REVERT: G 135 MET cc_start: 0.8450 (mmm) cc_final: 0.8212 (mmm) REVERT: G 160 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.4269 (tt0) REVERT: G 210 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: G 326 HIS cc_start: 0.8368 (t70) cc_final: 0.8025 (t-170) REVERT: G 342 CYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7882 (p) outliers start: 129 outliers final: 89 residues processed: 330 average time/residue: 0.1160 time to fit residues: 61.5680 Evaluate side-chains 315 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 212 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 375 TYR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 0.0670 chunk 96 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.196433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.127985 restraints weight = 27150.694| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.05 r_work: 0.3565 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20153 Z= 0.128 Angle : 0.625 11.445 27321 Z= 0.306 Chirality : 0.040 0.458 3122 Planarity : 0.005 0.072 3458 Dihedral : 5.788 57.018 2816 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.83 % Allowed : 26.97 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2394 helix: 1.80 (0.13), residues: 1638 sheet: -1.00 (0.58), residues: 105 loop : -2.56 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 167 TYR 0.024 0.001 TYR B 136 PHE 0.032 0.001 PHE F 350 TRP 0.013 0.001 TRP B 115 HIS 0.002 0.000 HIS F 311 Details of bonding type rmsd covalent geometry : bond 0.00294 (20132) covalent geometry : angle 0.60923 (27272) SS BOND : bond 0.00284 ( 14) SS BOND : angle 0.51768 ( 28) hydrogen bonds : bond 0.03227 ( 1244) hydrogen bonds : angle 4.09788 ( 3669) link_NAG-ASN : bond 0.00782 ( 7) link_NAG-ASN : angle 5.15034 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 230 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8038 (mmt) cc_final: 0.7551 (mmt) REVERT: A 160 GLU cc_start: 0.4566 (OUTLIER) cc_final: 0.3973 (tt0) REVERT: A 210 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6003 (m-80) REVERT: A 326 HIS cc_start: 0.8340 (t70) cc_final: 0.8113 (t70) REVERT: A 332 THR cc_start: 0.4746 (OUTLIER) cc_final: 0.4454 (p) REVERT: B 51 ASP cc_start: 0.7607 (m-30) cc_final: 0.7333 (m-30) REVERT: B 190 ARG cc_start: 0.7897 (tmm160) cc_final: 0.6208 (mtm180) REVERT: B 334 ARG cc_start: 0.7553 (ptp90) cc_final: 0.7300 (ttp80) REVERT: B 359 LYS cc_start: 0.6466 (OUTLIER) cc_final: 0.6221 (mppt) REVERT: C 70 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8690 (m-10) REVERT: C 191 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 380 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7432 (mtm180) REVERT: D 135 MET cc_start: 0.8764 (tpp) cc_final: 0.8526 (mmm) REVERT: D 210 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: D 350 PHE cc_start: 0.7497 (m-80) cc_final: 0.7057 (m-80) REVERT: D 380 ARG cc_start: 0.7073 (mtt90) cc_final: 0.6262 (mtm180) REVERT: E 160 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.5134 (tt0) REVERT: E 210 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6850 (m-80) REVERT: E 326 HIS cc_start: 0.8196 (t70) cc_final: 0.7816 (t-170) REVERT: E 342 CYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7562 (p) REVERT: E 380 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7252 (mtm180) REVERT: F 160 GLU cc_start: 0.5229 (OUTLIER) cc_final: 0.4540 (tt0) REVERT: F 210 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: F 380 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7738 (mtt90) REVERT: G 42 LEU cc_start: 0.1112 (OUTLIER) cc_final: 0.0877 (pp) REVERT: G 160 GLU cc_start: 0.4937 (OUTLIER) cc_final: 0.4206 (tt0) REVERT: G 210 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: G 326 HIS cc_start: 0.8346 (t70) cc_final: 0.7994 (t-170) outliers start: 124 outliers final: 92 residues processed: 323 average time/residue: 0.1215 time to fit residues: 63.1529 Evaluate side-chains 323 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 217 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 52 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 170 optimal weight: 10.9990 chunk 179 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 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 = 0.4469 r_free = 0.4469 target = 0.196278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133486 restraints weight = 27051.338| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.73 r_work: 0.3510 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20153 Z= 0.135 Angle : 0.625 10.965 27321 Z= 0.306 Chirality : 0.041 0.445 3122 Planarity : 0.005 0.067 3458 Dihedral : 5.598 56.868 2816 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 6.02 % Allowed : 27.07 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2394 helix: 1.81 (0.13), residues: 1638 sheet: -0.90 (0.58), residues: 105 loop : -2.51 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 167 TYR 0.019 0.001 TYR B 213 PHE 0.023 0.001 PHE G 350 TRP 0.015 0.001 TRP B 115 HIS 0.003 0.000 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00317 (20132) covalent geometry : angle 0.60933 (27272) SS BOND : bond 0.00347 ( 14) SS BOND : angle 0.51815 ( 28) hydrogen bonds : bond 0.03264 ( 1244) hydrogen bonds : angle 4.11375 ( 3669) link_NAG-ASN : bond 0.00804 ( 7) link_NAG-ASN : angle 5.02671 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 230 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8131 (mmt) cc_final: 0.7830 (mmt) REVERT: A 160 GLU cc_start: 0.4568 (OUTLIER) cc_final: 0.4012 (tt0) REVERT: A 210 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6102 (m-80) REVERT: A 326 HIS cc_start: 0.8330 (t70) cc_final: 0.8104 (t70) REVERT: A 332 THR cc_start: 0.4890 (OUTLIER) cc_final: 0.4597 (p) REVERT: B 51 ASP cc_start: 0.7748 (m-30) cc_final: 0.7465 (m-30) REVERT: B 135 MET cc_start: 0.8768 (mmm) cc_final: 0.8397 (mmm) REVERT: B 190 ARG cc_start: 0.7310 (tmm160) cc_final: 0.6307 (mtm180) REVERT: B 334 ARG cc_start: 0.7602 (ptp90) cc_final: 0.7313 (ttp80) REVERT: B 359 LYS cc_start: 0.6266 (OUTLIER) cc_final: 0.5990 (mppt) REVERT: C 70 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8717 (m-10) REVERT: C 191 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7954 (tm-30) REVERT: D 135 MET cc_start: 0.8785 (tpp) cc_final: 0.8559 (mmm) REVERT: D 210 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7146 (m-80) REVERT: D 350 PHE cc_start: 0.7525 (m-80) cc_final: 0.7162 (m-80) REVERT: E 160 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.5074 (tt0) REVERT: E 210 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: E 326 HIS cc_start: 0.8190 (t70) cc_final: 0.7976 (t-170) REVERT: E 342 CYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7622 (p) REVERT: E 380 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7309 (mtm180) REVERT: F 160 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4424 (tt0) REVERT: F 210 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: F 326 HIS cc_start: 0.8157 (t70) cc_final: 0.7818 (t-170) REVERT: F 380 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7611 (mtt180) REVERT: G 42 LEU cc_start: 0.1095 (OUTLIER) cc_final: 0.0854 (pp) REVERT: G 160 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.4160 (tt0) REVERT: G 210 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: G 326 HIS cc_start: 0.8325 (t70) cc_final: 0.8008 (t-170) REVERT: G 380 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.7211 (mtm-85) outliers start: 128 outliers final: 101 residues processed: 323 average time/residue: 0.1242 time to fit residues: 64.0834 Evaluate side-chains 336 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 221 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 225 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 201 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 198 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 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 = 0.4471 r_free = 0.4471 target = 0.196137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128165 restraints weight = 26845.909| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.99 r_work: 0.3569 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20153 Z= 0.127 Angle : 0.622 10.589 27321 Z= 0.305 Chirality : 0.040 0.441 3122 Planarity : 0.005 0.070 3458 Dihedral : 5.410 56.434 2816 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.36 % Allowed : 27.82 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2394 helix: 1.85 (0.13), residues: 1638 sheet: -0.78 (0.59), residues: 105 loop : -2.51 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 380 TYR 0.020 0.001 TYR B 213 PHE 0.031 0.001 PHE F 350 TRP 0.014 0.001 TRP C 115 HIS 0.003 0.000 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00292 (20132) covalent geometry : angle 0.60836 (27272) SS BOND : bond 0.00283 ( 14) SS BOND : angle 0.53211 ( 28) hydrogen bonds : bond 0.03180 ( 1244) hydrogen bonds : angle 4.07577 ( 3669) link_NAG-ASN : bond 0.00758 ( 7) link_NAG-ASN : angle 4.68076 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 229 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4668 (OUTLIER) cc_final: 0.4046 (tt0) REVERT: A 210 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6055 (m-80) REVERT: A 326 HIS cc_start: 0.8441 (t70) cc_final: 0.8207 (t70) REVERT: A 332 THR cc_start: 0.4809 (OUTLIER) cc_final: 0.4497 (p) REVERT: B 51 ASP cc_start: 0.7762 (m-30) cc_final: 0.7485 (m-30) REVERT: B 190 ARG cc_start: 0.7355 (tmm160) cc_final: 0.6354 (mtm180) REVERT: B 334 ARG cc_start: 0.7582 (ptp90) cc_final: 0.7330 (ttp80) REVERT: B 359 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5953 (mppt) REVERT: C 70 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8698 (m-10) REVERT: C 191 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7900 (tm-30) REVERT: C 342 CYS cc_start: 0.8741 (t) cc_final: 0.7744 (p) REVERT: D 135 MET cc_start: 0.8751 (tpp) cc_final: 0.8547 (mmm) REVERT: D 210 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: D 350 PHE cc_start: 0.7521 (m-80) cc_final: 0.7167 (m-80) REVERT: E 160 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5121 (tt0) REVERT: E 210 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: E 326 HIS cc_start: 0.8248 (t70) cc_final: 0.8020 (t-170) REVERT: E 342 CYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7592 (p) REVERT: E 380 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7381 (mtm180) REVERT: F 160 GLU cc_start: 0.5167 (OUTLIER) cc_final: 0.4463 (tt0) REVERT: F 210 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6236 (m-80) REVERT: F 326 HIS cc_start: 0.8222 (t70) cc_final: 0.7868 (t-170) REVERT: F 380 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7583 (mtt180) REVERT: G 42 LEU cc_start: 0.1148 (OUTLIER) cc_final: 0.0909 (pp) REVERT: G 135 MET cc_start: 0.8554 (mmm) cc_final: 0.8254 (mmm) REVERT: G 160 GLU cc_start: 0.4909 (OUTLIER) cc_final: 0.4212 (tt0) REVERT: G 210 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: G 326 HIS cc_start: 0.8397 (t70) cc_final: 0.8095 (t-170) REVERT: G 380 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7206 (mtm-85) outliers start: 114 outliers final: 94 residues processed: 316 average time/residue: 0.1244 time to fit residues: 63.1946 Evaluate side-chains 325 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 217 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS B 163 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 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 = 0.4420 r_free = 0.4420 target = 0.189328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.122882 restraints weight = 27251.477| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.79 r_work: 0.3513 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 20153 Z= 0.223 Angle : 0.700 10.739 27321 Z= 0.344 Chirality : 0.043 0.460 3122 Planarity : 0.005 0.067 3458 Dihedral : 5.715 59.790 2816 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.59 % Allowed : 27.44 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2394 helix: 1.66 (0.13), residues: 1624 sheet: -1.18 (0.56), residues: 105 loop : -2.57 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 167 TYR 0.024 0.002 TYR B 213 PHE 0.033 0.002 PHE G 350 TRP 0.022 0.002 TRP B 115 HIS 0.003 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00540 (20132) covalent geometry : angle 0.68716 (27272) SS BOND : bond 0.00615 ( 14) SS BOND : angle 0.64898 ( 28) hydrogen bonds : bond 0.03801 ( 1244) hydrogen bonds : angle 4.35688 ( 3669) link_NAG-ASN : bond 0.00925 ( 7) link_NAG-ASN : angle 4.88353 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 216 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.4636 (OUTLIER) cc_final: 0.4196 (tt0) REVERT: A 210 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6212 (m-80) REVERT: A 326 HIS cc_start: 0.8544 (t70) cc_final: 0.8296 (t70) REVERT: A 332 THR cc_start: 0.5032 (OUTLIER) cc_final: 0.4734 (p) REVERT: A 380 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7449 (mtt90) REVERT: B 51 ASP cc_start: 0.8010 (m-30) cc_final: 0.7655 (m-30) REVERT: B 135 MET cc_start: 0.8763 (mmm) cc_final: 0.8443 (mmm) REVERT: B 334 ARG cc_start: 0.7630 (ptp90) cc_final: 0.7318 (ttp80) REVERT: B 359 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.6053 (mppt) REVERT: C 135 MET cc_start: 0.8993 (tpp) cc_final: 0.8669 (mmm) REVERT: C 191 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7918 (tm-30) REVERT: D 135 MET cc_start: 0.8921 (tpp) cc_final: 0.8637 (mmm) REVERT: D 210 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: D 350 PHE cc_start: 0.7599 (m-80) cc_final: 0.7268 (m-80) REVERT: E 160 GLU cc_start: 0.5456 (OUTLIER) cc_final: 0.4839 (tt0) REVERT: E 210 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.6520 (m-80) REVERT: E 326 HIS cc_start: 0.8361 (t70) cc_final: 0.8110 (t-170) REVERT: E 380 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7602 (mtm-85) REVERT: F 160 GLU cc_start: 0.5410 (OUTLIER) cc_final: 0.4626 (tt0) REVERT: F 210 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: F 326 HIS cc_start: 0.8307 (t70) cc_final: 0.7946 (t-170) REVERT: F 380 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7713 (mtt180) REVERT: G 42 LEU cc_start: 0.1084 (OUTLIER) cc_final: 0.0850 (pp) REVERT: G 135 MET cc_start: 0.8649 (mmm) cc_final: 0.8432 (mmm) REVERT: G 160 GLU cc_start: 0.5235 (OUTLIER) cc_final: 0.4474 (tt0) REVERT: G 210 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: G 326 HIS cc_start: 0.8512 (t70) cc_final: 0.8188 (t-170) outliers start: 119 outliers final: 99 residues processed: 307 average time/residue: 0.1162 time to fit residues: 58.1454 Evaluate side-chains 321 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 210 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 115 TRP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 115 TRP Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 357 HIS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 234 ILE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 115 TRP Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 160 GLU Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 278 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 73 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.192548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.127679 restraints weight = 27003.213| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.44 r_work: 0.3532 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20153 Z= 0.142 Angle : 0.644 10.138 27321 Z= 0.316 Chirality : 0.041 0.423 3122 Planarity : 0.005 0.063 3458 Dihedral : 5.515 57.831 2816 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.17 % Allowed : 28.24 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 2394 helix: 1.72 (0.13), residues: 1638 sheet: -1.03 (0.57), residues: 105 loop : -2.56 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 380 TYR 0.019 0.001 TYR B 213 PHE 0.030 0.001 PHE F 350 TRP 0.018 0.002 TRP B 115 HIS 0.003 0.000 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00335 (20132) covalent geometry : angle 0.63208 (27272) SS BOND : bond 0.00357 ( 14) SS BOND : angle 0.57968 ( 28) hydrogen bonds : bond 0.03364 ( 1244) hydrogen bonds : angle 4.19805 ( 3669) link_NAG-ASN : bond 0.00732 ( 7) link_NAG-ASN : angle 4.46740 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4762.11 seconds wall clock time: 82 minutes 38.32 seconds (4958.32 seconds total)