Starting phenix.real_space_refine on Thu Mar 5 08:06:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbf_21588/03_2026/6wbf_21588.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbf_21588/03_2026/6wbf_21588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wbf_21588/03_2026/6wbf_21588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbf_21588/03_2026/6wbf_21588.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbf_21588/03_2026/6wbf_21588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbf_21588/03_2026/6wbf_21588.cif" } resolution = 2.83 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 77 5.16 5 C 13321 2.51 5 N 2912 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "F" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.92, per 1000 atoms: 0.25 Number of scatterers: 19712 At special positions: 0 Unit cell: (107.73, 108.756, 121.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 21 15.00 O 3381 8.00 N 2912 7.00 C 13321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " 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 407 " - " ASN A 255 " " NAG B 407 " - " ASN B 255 " " NAG C 407 " - " ASN C 255 " " NAG D 407 " - " ASN D 255 " " NAG E 407 " - " ASN E 255 " " NAG F 407 " - " ASN F 255 " " NAG G 407 " - " ASN G 255 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 944.0 milliseconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 70.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.629A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.950A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 131 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.620A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.717A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.831A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.680A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.631A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.948A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix removed outlier: 3.719A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 304 through 312 removed outlier: 4.014A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.828A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.681A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.628A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.949A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix removed outlier: 3.717A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.829A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.630A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 99 through 108 removed outlier: 3.950A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.618A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.717A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.829A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.681A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.630A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 99 through 108 removed outlier: 3.950A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.618A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix removed outlier: 3.717A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 304 through 312 removed outlier: 4.012A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.829A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.628A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.948A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.618A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 3.716A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.830A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.631A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.950A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix removed outlier: 3.718A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 304 through 312 removed outlier: 4.012A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.829A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.681A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 1226 hydrogen bonds defined for protein. 3531 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: 3.30 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2895 1.32 - 1.44: 5035 1.44 - 1.57: 12083 1.57 - 1.69: 42 1.69 - 1.81: 91 Bond restraints: 20146 Sorted by residual: bond pdb=" N ASN A 369 " pdb=" CA ASN A 369 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.17e-02 7.31e+03 9.38e+00 bond pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.17e-02 7.31e+03 8.66e+00 bond pdb=" N ASN C 369 " pdb=" CA ASN C 369 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.17e-02 7.31e+03 8.62e+00 bond pdb=" N ASN D 369 " pdb=" CA ASN D 369 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.44e+00 bond pdb=" N ASN G 369 " pdb=" CA ASN G 369 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.11e+00 ... (remaining 20141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 26501 2.02 - 4.04: 708 4.04 - 6.05: 91 6.05 - 8.07: 14 8.07 - 10.09: 14 Bond angle restraints: 27328 Sorted by residual: angle pdb=" C TYR E 10 " pdb=" N VAL E 11 " pdb=" CA VAL E 11 " ideal model delta sigma weight residual 122.77 118.80 3.97 1.05e+00 9.07e-01 1.43e+01 angle pdb=" C TYR B 10 " pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 122.77 118.88 3.89 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C TYR D 10 " pdb=" N VAL D 11 " pdb=" CA VAL D 11 " ideal model delta sigma weight residual 122.77 118.91 3.86 1.05e+00 9.07e-01 1.35e+01 angle pdb=" C TYR F 10 " pdb=" N VAL F 11 " pdb=" CA VAL F 11 " ideal model delta sigma weight residual 122.77 118.91 3.86 1.05e+00 9.07e-01 1.35e+01 angle pdb=" C TYR A 10 " pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 122.77 118.92 3.85 1.05e+00 9.07e-01 1.34e+01 ... (remaining 27323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.69: 12379 29.69 - 59.39: 622 59.39 - 89.08: 32 89.08 - 118.77: 1 118.77 - 148.47: 14 Dihedral angle restraints: 13048 sinusoidal: 5873 harmonic: 7175 Sorted by residual: dihedral pdb=" N1 PTY A 401 " pdb=" C2 PTY A 401 " pdb=" C3 PTY A 401 " pdb=" O11 PTY A 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.14 148.47 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N1 PTY D 401 " pdb=" C2 PTY D 401 " pdb=" C3 PTY D 401 " pdb=" O11 PTY D 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.11 148.44 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N1 PTY B 401 " pdb=" C2 PTY B 401 " pdb=" C3 PTY B 401 " pdb=" O11 PTY B 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.09 148.42 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 13045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2253 0.038 - 0.076: 719 0.076 - 0.114: 228 0.114 - 0.152: 41 0.152 - 0.191: 14 Chirality restraints: 3255 Sorted by residual: chirality pdb=" CA ILE E 373 " pdb=" N ILE E 373 " pdb=" C ILE E 373 " pdb=" CB ILE E 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ILE D 373 " pdb=" N ILE D 373 " pdb=" C ILE D 373 " pdb=" CB ILE D 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA ILE A 373 " pdb=" N ILE A 373 " pdb=" C ILE A 373 " pdb=" CB ILE A 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 3252 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 407 " -0.090 2.00e-02 2.50e+03 7.40e-02 6.84e+01 pdb=" C7 NAG G 407 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG G 407 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG G 407 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG G 407 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 407 " 0.090 2.00e-02 2.50e+03 7.39e-02 6.84e+01 pdb=" C7 NAG F 407 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG F 407 " 0.069 2.00e-02 2.50e+03 pdb=" N2 NAG F 407 " -0.117 2.00e-02 2.50e+03 pdb=" O7 NAG F 407 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 407 " -0.090 2.00e-02 2.50e+03 7.39e-02 6.82e+01 pdb=" C7 NAG B 407 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG B 407 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG B 407 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG B 407 " 0.016 2.00e-02 2.50e+03 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1397 2.73 - 3.27: 20875 3.27 - 3.81: 33222 3.81 - 4.36: 39530 4.36 - 4.90: 68959 Nonbonded interactions: 163983 Sorted by model distance: nonbonded pdb=" O LEU A 52 " pdb=" OH TYR G 111 " model vdw 2.183 3.040 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.193 3.040 ... (remaining 163978 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: 0.05 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: 1.010 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.920 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 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 : 0.007 0.049 20167 Z= 0.341 Angle : 0.826 10.089 27377 Z= 0.455 Chirality : 0.043 0.191 3255 Planarity : 0.005 0.074 3178 Dihedral : 16.595 148.466 8344 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.38 % Allowed : 6.14 % Favored : 93.48 % 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: -1.45 (0.16), residues: 2380 helix: -0.08 (0.12), residues: 1603 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 152 TYR 0.015 0.001 TYR E 10 PHE 0.013 0.002 PHE B 54 TRP 0.008 0.001 TRP A 104 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00699 (20146) covalent geometry : angle 0.82613 (27328) SS BOND : bond 0.00264 ( 14) SS BOND : angle 0.72614 ( 28) hydrogen bonds : bond 0.14007 ( 1226) hydrogen bonds : angle 5.41394 ( 3531) link_NAG-ASN : bond 0.00610 ( 7) link_NAG-ASN : angle 0.87820 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 517 time to evaluate : 0.766 Fit side-chains REVERT: A 9 GLU cc_start: 0.6351 (tt0) cc_final: 0.5963 (mm-30) REVERT: A 35 ASP cc_start: 0.6726 (m-30) cc_final: 0.6444 (m-30) REVERT: A 56 GLN cc_start: 0.6870 (tp-100) cc_final: 0.6250 (tt0) REVERT: A 65 SER cc_start: 0.8400 (m) cc_final: 0.7727 (p) REVERT: A 74 TRP cc_start: 0.7067 (t60) cc_final: 0.6512 (t-100) REVERT: A 100 ASN cc_start: 0.7285 (m-40) cc_final: 0.7046 (m110) REVERT: A 111 TYR cc_start: 0.7491 (m-10) cc_final: 0.6300 (m-10) REVERT: A 135 ILE cc_start: 0.6230 (tt) cc_final: 0.6008 (mt) REVERT: A 201 LYS cc_start: 0.6877 (tppp) cc_final: 0.6640 (tppt) REVERT: A 208 ASN cc_start: 0.5723 (t0) cc_final: 0.5456 (t0) REVERT: A 212 LYS cc_start: 0.5550 (mttt) cc_final: 0.5226 (mttp) REVERT: A 254 ARG cc_start: 0.6826 (ttm110) cc_final: 0.6586 (ttm-80) REVERT: A 338 ASN cc_start: 0.6514 (m-40) cc_final: 0.6288 (m-40) REVERT: A 348 LEU cc_start: 0.6310 (mt) cc_final: 0.6001 (mt) REVERT: B 35 ASP cc_start: 0.6571 (m-30) cc_final: 0.6205 (m-30) REVERT: B 56 GLN cc_start: 0.6777 (tp-100) cc_final: 0.6083 (tt0) REVERT: B 74 TRP cc_start: 0.7493 (t60) cc_final: 0.7062 (t-100) REVERT: B 100 ASN cc_start: 0.7434 (m-40) cc_final: 0.6471 (t0) REVERT: B 111 TYR cc_start: 0.7354 (m-10) cc_final: 0.6153 (m-10) REVERT: B 129 PHE cc_start: 0.8078 (m-80) cc_final: 0.7876 (m-80) REVERT: B 135 ILE cc_start: 0.6221 (tt) cc_final: 0.5865 (mt) REVERT: B 201 LYS cc_start: 0.6843 (tppp) cc_final: 0.6581 (tppt) REVERT: B 217 ARG cc_start: 0.6654 (mmp-170) cc_final: 0.6387 (mmp80) REVERT: B 219 LEU cc_start: 0.6726 (mp) cc_final: 0.6474 (mp) REVERT: B 229 ILE cc_start: 0.7415 (mt) cc_final: 0.7153 (mm) REVERT: B 242 ASP cc_start: 0.7737 (p0) cc_final: 0.7521 (p0) REVERT: B 254 ARG cc_start: 0.6805 (ttm110) cc_final: 0.6509 (ttt180) REVERT: B 262 GLN cc_start: 0.8084 (pt0) cc_final: 0.7859 (pt0) REVERT: B 348 LEU cc_start: 0.6460 (mt) cc_final: 0.6252 (mt) REVERT: C 35 ASP cc_start: 0.6476 (m-30) cc_final: 0.6220 (m-30) REVERT: C 74 TRP cc_start: 0.7291 (t60) cc_final: 0.6554 (t-100) REVERT: C 100 ASN cc_start: 0.7341 (m-40) cc_final: 0.6279 (t0) REVERT: C 111 TYR cc_start: 0.7236 (m-10) cc_final: 0.5993 (m-10) REVERT: C 139 LEU cc_start: 0.5468 (tp) cc_final: 0.5228 (tp) REVERT: C 201 LYS cc_start: 0.6764 (tppp) cc_final: 0.6360 (tmmt) REVERT: C 208 ASN cc_start: 0.5808 (t0) cc_final: 0.5596 (t0) REVERT: C 222 ILE cc_start: 0.7129 (mm) cc_final: 0.6892 (mt) REVERT: C 229 ILE cc_start: 0.7416 (mt) cc_final: 0.7133 (mm) REVERT: C 254 ARG cc_start: 0.6905 (ttm110) cc_final: 0.6658 (ttm-80) REVERT: C 299 PHE cc_start: 0.6183 (t80) cc_final: 0.5715 (t80) REVERT: C 345 TYR cc_start: 0.7119 (t80) cc_final: 0.6813 (t80) REVERT: D 9 GLU cc_start: 0.6323 (tt0) cc_final: 0.5933 (mm-30) REVERT: D 35 ASP cc_start: 0.6595 (m-30) cc_final: 0.6231 (m-30) REVERT: D 36 LYS cc_start: 0.6543 (ttmm) cc_final: 0.6309 (ttmt) REVERT: D 50 ILE cc_start: 0.7160 (mt) cc_final: 0.6943 (mm) REVERT: D 56 GLN cc_start: 0.6961 (tp-100) cc_final: 0.6289 (tt0) REVERT: D 74 TRP cc_start: 0.7263 (t60) cc_final: 0.6857 (t-100) REVERT: D 100 ASN cc_start: 0.7333 (m-40) cc_final: 0.6412 (t0) REVERT: D 111 TYR cc_start: 0.7226 (m-10) cc_final: 0.6016 (m-10) REVERT: D 201 LYS cc_start: 0.6509 (tppp) cc_final: 0.6287 (tppt) REVERT: D 208 ASN cc_start: 0.5939 (t0) cc_final: 0.5680 (t0) REVERT: D 212 LYS cc_start: 0.5851 (mttt) cc_final: 0.5580 (mttp) REVERT: D 229 ILE cc_start: 0.7671 (mt) cc_final: 0.7449 (mm) REVERT: D 254 ARG cc_start: 0.6806 (ttm110) cc_final: 0.6423 (ttm-80) REVERT: D 262 GLN cc_start: 0.8155 (pt0) cc_final: 0.7931 (pt0) REVERT: D 296 PHE cc_start: 0.7139 (m-80) cc_final: 0.6788 (m-80) REVERT: D 338 ASN cc_start: 0.6740 (m-40) cc_final: 0.6535 (m-40) REVERT: E 36 LYS cc_start: 0.6210 (ttmm) cc_final: 0.5612 (ttpt) REVERT: E 65 SER cc_start: 0.8369 (m) cc_final: 0.7706 (p) REVERT: E 74 TRP cc_start: 0.7355 (t60) cc_final: 0.6996 (t-100) REVERT: E 100 ASN cc_start: 0.7525 (m-40) cc_final: 0.6344 (t0) REVERT: E 111 TYR cc_start: 0.7330 (m-10) cc_final: 0.6215 (m-10) REVERT: E 129 PHE cc_start: 0.8093 (m-80) cc_final: 0.7664 (m-80) REVERT: E 135 ILE cc_start: 0.6353 (tt) cc_final: 0.6078 (mt) REVERT: E 139 LEU cc_start: 0.5757 (tp) cc_final: 0.5347 (tp) REVERT: E 201 LYS cc_start: 0.6866 (tppp) cc_final: 0.6496 (tmmt) REVERT: E 222 ILE cc_start: 0.7367 (mm) cc_final: 0.7009 (mt) REVERT: E 229 ILE cc_start: 0.7596 (mt) cc_final: 0.7343 (mm) REVERT: E 254 ARG cc_start: 0.6777 (ttm110) cc_final: 0.6447 (ttm-80) REVERT: E 262 GLN cc_start: 0.8199 (pt0) cc_final: 0.7983 (pt0) REVERT: E 296 PHE cc_start: 0.7097 (m-80) cc_final: 0.6812 (m-80) REVERT: F 31 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6795 (tt0) REVERT: F 35 ASP cc_start: 0.6668 (m-30) cc_final: 0.6464 (m-30) REVERT: F 100 ASN cc_start: 0.7339 (m-40) cc_final: 0.6533 (t0) REVERT: F 111 TYR cc_start: 0.7294 (m-10) cc_final: 0.5963 (m-10) REVERT: F 139 LEU cc_start: 0.5547 (tp) cc_final: 0.5287 (tp) REVERT: F 201 LYS cc_start: 0.6588 (tppp) cc_final: 0.6231 (tmmt) REVERT: F 212 LYS cc_start: 0.5669 (mttt) cc_final: 0.5452 (mttp) REVERT: F 229 ILE cc_start: 0.7753 (mt) cc_final: 0.7494 (mm) REVERT: F 254 ARG cc_start: 0.6744 (ttm110) cc_final: 0.6433 (ttt180) REVERT: F 262 GLN cc_start: 0.8118 (pt0) cc_final: 0.7908 (pt0) REVERT: G 5 GLN cc_start: 0.6075 (mt0) cc_final: 0.5854 (tp40) REVERT: G 9 GLU cc_start: 0.6184 (tt0) cc_final: 0.5947 (mp0) REVERT: G 50 ILE cc_start: 0.7297 (mt) cc_final: 0.7089 (mm) REVERT: G 75 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7225 (mmt180) REVERT: G 100 ASN cc_start: 0.7452 (m-40) cc_final: 0.6474 (t0) REVERT: G 111 TYR cc_start: 0.7407 (m-10) cc_final: 0.6251 (m-10) REVERT: G 201 LYS cc_start: 0.6611 (tppp) cc_final: 0.6342 (tppt) REVERT: G 217 ARG cc_start: 0.6817 (mmp-170) cc_final: 0.6549 (mmp80) REVERT: G 219 LEU cc_start: 0.6619 (mp) cc_final: 0.6377 (mt) REVERT: G 222 ILE cc_start: 0.6956 (mm) cc_final: 0.6571 (mp) REVERT: G 229 ILE cc_start: 0.7855 (mt) cc_final: 0.7597 (mp) REVERT: G 254 ARG cc_start: 0.7049 (ttm110) cc_final: 0.6641 (ttm-80) REVERT: G 296 PHE cc_start: 0.7006 (m-80) cc_final: 0.6068 (m-80) REVERT: G 338 ASN cc_start: 0.6838 (m-40) cc_final: 0.6504 (m-40) outliers start: 7 outliers final: 0 residues processed: 521 average time/residue: 0.5993 time to fit residues: 353.9609 Evaluate side-chains 375 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 89 GLN A 90 GLN A 92 ASN A 274 GLN A 353 ASN B 76 GLN B 89 GLN B 274 GLN B 353 ASN C 76 GLN C 89 GLN C 90 GLN C 92 ASN C 274 GLN D 76 GLN D 89 GLN D 90 GLN D 92 ASN D 274 GLN D 353 ASN E 76 GLN E 89 GLN E 274 GLN E 326 ASN F 76 GLN F 90 GLN F 274 GLN F 326 ASN F 353 ASN G 76 GLN G 89 GLN G 90 GLN G 134 HIS G 274 GLN G 326 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.184248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133726 restraints weight = 19387.424| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.62 r_work: 0.3356 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20167 Z= 0.142 Angle : 0.642 8.983 27377 Z= 0.305 Chirality : 0.040 0.141 3255 Planarity : 0.004 0.040 3178 Dihedral : 14.996 121.460 4522 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.59 % Allowed : 14.61 % Favored : 81.80 % 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: 0.48 (0.18), residues: 2380 helix: 1.47 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.34 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 128 TYR 0.012 0.002 TYR G 230 PHE 0.013 0.002 PHE E 141 TRP 0.013 0.001 TRP G 74 HIS 0.004 0.002 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00320 (20146) covalent geometry : angle 0.63980 (27328) SS BOND : bond 0.00323 ( 14) SS BOND : angle 0.79027 ( 28) hydrogen bonds : bond 0.04016 ( 1226) hydrogen bonds : angle 4.09482 ( 3531) link_NAG-ASN : bond 0.00694 ( 7) link_NAG-ASN : angle 1.88134 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 409 time to evaluate : 0.786 Fit side-chains REVERT: A 9 GLU cc_start: 0.7499 (tt0) cc_final: 0.7007 (mm-30) REVERT: A 65 SER cc_start: 0.9031 (m) cc_final: 0.8700 (p) REVERT: A 100 ASN cc_start: 0.7780 (m-40) cc_final: 0.6615 (t0) REVERT: A 201 LYS cc_start: 0.7032 (tppp) cc_final: 0.6813 (tppt) REVERT: A 208 ASN cc_start: 0.6432 (t0) cc_final: 0.6190 (t0) REVERT: A 212 LYS cc_start: 0.6746 (mttt) cc_final: 0.6367 (mttp) REVERT: A 307 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6605 (tppp) REVERT: A 348 LEU cc_start: 0.7206 (mt) cc_final: 0.6968 (mt) REVERT: B 9 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6724 (mm-30) REVERT: B 35 ASP cc_start: 0.7359 (m-30) cc_final: 0.6795 (m-30) REVERT: B 70 SER cc_start: 0.7864 (p) cc_final: 0.7627 (m) REVERT: B 75 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8346 (mmt90) REVERT: B 100 ASN cc_start: 0.7503 (m-40) cc_final: 0.6465 (t0) REVERT: B 129 PHE cc_start: 0.8429 (m-80) cc_final: 0.8185 (m-80) REVERT: B 262 GLN cc_start: 0.8626 (pt0) cc_final: 0.8380 (pt0) REVERT: C 9 GLU cc_start: 0.7691 (mt-10) cc_final: 0.6654 (mm-30) REVERT: C 35 ASP cc_start: 0.7263 (m-30) cc_final: 0.6706 (m-30) REVERT: C 100 ASN cc_start: 0.8059 (m-40) cc_final: 0.6831 (t0) REVERT: C 128 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7929 (tmm160) REVERT: C 201 LYS cc_start: 0.7054 (tppp) cc_final: 0.6731 (tmmt) REVERT: C 208 ASN cc_start: 0.6631 (t0) cc_final: 0.6164 (t0) REVERT: C 222 ILE cc_start: 0.7774 (mm) cc_final: 0.7542 (mt) REVERT: C 229 ILE cc_start: 0.8475 (mt) cc_final: 0.8207 (mm) REVERT: C 296 PHE cc_start: 0.7458 (m-80) cc_final: 0.7174 (m-80) REVERT: C 299 PHE cc_start: 0.6385 (t80) cc_final: 0.5752 (t80) REVERT: C 355 LYS cc_start: 0.5528 (mtpt) cc_final: 0.4800 (mmpt) REVERT: D 9 GLU cc_start: 0.7537 (tt0) cc_final: 0.7036 (mm-30) REVERT: D 75 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8277 (mmt180) REVERT: D 100 ASN cc_start: 0.7960 (m-40) cc_final: 0.6871 (t0) REVERT: D 208 ASN cc_start: 0.6382 (t0) cc_final: 0.6047 (t0) REVERT: D 214 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7596 (mm) REVERT: D 219 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7298 (mp) REVERT: D 229 ILE cc_start: 0.8435 (mt) cc_final: 0.8199 (mm) REVERT: D 254 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7171 (ttm-80) REVERT: D 262 GLN cc_start: 0.8487 (pt0) cc_final: 0.8257 (pt0) REVERT: D 355 LYS cc_start: 0.6320 (mtpp) cc_final: 0.5783 (mtmp) REVERT: E 36 LYS cc_start: 0.7335 (ttmm) cc_final: 0.6654 (ttpt) REVERT: E 65 SER cc_start: 0.8991 (m) cc_final: 0.8739 (p) REVERT: E 100 ASN cc_start: 0.8128 (m-40) cc_final: 0.6801 (t0) REVERT: E 139 LEU cc_start: 0.6588 (tp) cc_final: 0.6182 (tp) REVERT: E 201 LYS cc_start: 0.7044 (tppp) cc_final: 0.6757 (tmmt) REVERT: E 222 ILE cc_start: 0.8043 (mm) cc_final: 0.7780 (mt) REVERT: E 254 ARG cc_start: 0.7266 (ttm110) cc_final: 0.7036 (ttm-80) REVERT: E 262 GLN cc_start: 0.8639 (pt0) cc_final: 0.8417 (pt0) REVERT: E 307 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6683 (tppp) REVERT: E 343 LYS cc_start: 0.5914 (pttp) cc_final: 0.5418 (mmmt) REVERT: E 355 LYS cc_start: 0.6131 (mtpm) cc_final: 0.5718 (mtmp) REVERT: F 9 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6619 (mm-30) REVERT: F 31 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7235 (tt0) REVERT: F 36 LYS cc_start: 0.7431 (ttmt) cc_final: 0.7201 (ttmt) REVERT: F 100 ASN cc_start: 0.8162 (m-40) cc_final: 0.6839 (t0) REVERT: F 139 LEU cc_start: 0.6596 (tp) cc_final: 0.6317 (tp) REVERT: F 201 LYS cc_start: 0.6899 (tppp) cc_final: 0.6629 (tmmt) REVERT: F 222 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7617 (mp) REVERT: F 229 ILE cc_start: 0.8470 (mt) cc_final: 0.8211 (mm) REVERT: F 254 ARG cc_start: 0.7264 (ttm110) cc_final: 0.6913 (mtt-85) REVERT: F 299 PHE cc_start: 0.6536 (t80) cc_final: 0.6008 (t80) REVERT: G 9 GLU cc_start: 0.7295 (tt0) cc_final: 0.6967 (mp0) REVERT: G 100 ASN cc_start: 0.8129 (m-40) cc_final: 0.6940 (t0) REVERT: G 139 LEU cc_start: 0.6521 (tp) cc_final: 0.6255 (tp) REVERT: G 222 ILE cc_start: 0.7738 (mm) cc_final: 0.7478 (mt) REVERT: G 254 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7237 (ttm-80) REVERT: G 345 TYR cc_start: 0.7513 (t80) cc_final: 0.7289 (t80) outliers start: 66 outliers final: 8 residues processed: 456 average time/residue: 0.5596 time to fit residues: 291.2126 Evaluate side-chains 345 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 332 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 307 LYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 349 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 134 HIS A 338 ASN B 326 ASN B 338 ASN B 353 ASN C 89 GLN C 338 ASN D 89 GLN D 92 ASN D 338 ASN E 326 ASN E 338 ASN F 89 GLN F 326 ASN F 338 ASN G 92 ASN G 326 ASN G 353 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.177658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134370 restraints weight = 19398.801| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.42 r_work: 0.3270 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20167 Z= 0.206 Angle : 0.689 8.543 27377 Z= 0.331 Chirality : 0.042 0.139 3255 Planarity : 0.004 0.040 3178 Dihedral : 13.654 82.353 4522 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.92 % Allowed : 15.37 % Favored : 78.71 % 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: 0.81 (0.18), residues: 2380 helix: 1.67 (0.13), residues: 1582 sheet: -0.66 (0.50), residues: 91 loop : -1.98 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 254 TYR 0.014 0.002 TYR C 230 PHE 0.021 0.002 PHE G 67 TRP 0.036 0.003 TRP G 74 HIS 0.007 0.002 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00499 (20146) covalent geometry : angle 0.68648 (27328) SS BOND : bond 0.00384 ( 14) SS BOND : angle 0.92026 ( 28) hydrogen bonds : bond 0.04503 ( 1226) hydrogen bonds : angle 4.23712 ( 3531) link_NAG-ASN : bond 0.00639 ( 7) link_NAG-ASN : angle 2.12231 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 345 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7825 (tt0) cc_final: 0.7520 (mt-10) REVERT: A 56 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7209 (tt0) REVERT: A 65 SER cc_start: 0.8781 (m) cc_final: 0.8574 (p) REVERT: A 89 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: A 100 ASN cc_start: 0.7855 (m-40) cc_final: 0.7490 (m-40) REVERT: A 135 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7099 (tt) REVERT: A 201 LYS cc_start: 0.7266 (tppp) cc_final: 0.6846 (tmtt) REVERT: A 207 ASN cc_start: 0.7273 (p0) cc_final: 0.7049 (p0) REVERT: A 208 ASN cc_start: 0.6659 (t0) cc_final: 0.6452 (t0) REVERT: A 222 ILE cc_start: 0.8247 (mt) cc_final: 0.8025 (mt) REVERT: A 348 LEU cc_start: 0.7608 (mt) cc_final: 0.7376 (mt) REVERT: B 70 SER cc_start: 0.8142 (p) cc_final: 0.7780 (m) REVERT: B 89 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: B 100 ASN cc_start: 0.7782 (m-40) cc_final: 0.6939 (t0) REVERT: B 222 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7718 (mt) REVERT: C 35 ASP cc_start: 0.7514 (m-30) cc_final: 0.7211 (m-30) REVERT: C 56 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: C 100 ASN cc_start: 0.7888 (m-40) cc_final: 0.6768 (t0) REVERT: C 201 LYS cc_start: 0.7315 (tppp) cc_final: 0.7057 (tmmt) REVERT: C 243 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8219 (mt-10) REVERT: C 296 PHE cc_start: 0.7550 (m-80) cc_final: 0.7341 (m-80) REVERT: C 299 PHE cc_start: 0.6519 (t80) cc_final: 0.5820 (t80) REVERT: C 355 LYS cc_start: 0.5591 (mtpt) cc_final: 0.5012 (mmpt) REVERT: D 100 ASN cc_start: 0.7979 (m-40) cc_final: 0.7033 (t0) REVERT: D 208 ASN cc_start: 0.6835 (t0) cc_final: 0.6453 (t0) REVERT: D 222 ILE cc_start: 0.8150 (mt) cc_final: 0.7915 (mt) REVERT: D 254 ARG cc_start: 0.7511 (ttm110) cc_final: 0.7111 (mtt-85) REVERT: D 343 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.5052 (mmtm) REVERT: E 36 LYS cc_start: 0.7585 (ttmm) cc_final: 0.6898 (ttpt) REVERT: E 88 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8307 (m) REVERT: E 89 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: E 100 ASN cc_start: 0.8036 (m-40) cc_final: 0.7518 (m-40) REVERT: E 129 PHE cc_start: 0.8540 (m-80) cc_final: 0.8331 (m-80) REVERT: E 135 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7066 (tt) REVERT: E 139 LEU cc_start: 0.7057 (tp) cc_final: 0.6739 (tp) REVERT: E 201 LYS cc_start: 0.7059 (tppp) cc_final: 0.6809 (tmmt) REVERT: E 222 ILE cc_start: 0.8086 (mm) cc_final: 0.7842 (mt) REVERT: E 254 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7274 (ttm-80) REVERT: E 343 LYS cc_start: 0.6064 (pttp) cc_final: 0.5716 (mmmt) REVERT: E 355 LYS cc_start: 0.6301 (mtpm) cc_final: 0.5699 (mtmp) REVERT: F 9 GLU cc_start: 0.7703 (mt-10) cc_final: 0.6827 (mm-30) REVERT: F 31 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7449 (tt0) REVERT: F 36 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7440 (ttmt) REVERT: F 81 ASP cc_start: 0.8431 (m-30) cc_final: 0.8191 (m-30) REVERT: F 100 ASN cc_start: 0.8110 (m-40) cc_final: 0.7037 (t0) REVERT: F 201 LYS cc_start: 0.7196 (tppp) cc_final: 0.6928 (tmmt) REVERT: F 222 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7666 (mt) REVERT: F 242 ASP cc_start: 0.8598 (p0) cc_final: 0.8167 (p0) REVERT: F 254 ARG cc_start: 0.7368 (ttm110) cc_final: 0.7062 (mtt-85) REVERT: G 89 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: G 100 ASN cc_start: 0.8040 (m-40) cc_final: 0.6985 (t0) REVERT: G 208 ASN cc_start: 0.6740 (t0) cc_final: 0.6290 (t0) REVERT: G 222 ILE cc_start: 0.8008 (mm) cc_final: 0.7789 (mt) outliers start: 109 outliers final: 34 residues processed: 422 average time/residue: 0.5390 time to fit residues: 260.6875 Evaluate side-chains 365 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 320 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 343 LYS Chi-restraints excluded: chain G residue 349 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 25 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 338 ASN B 338 ASN C 89 GLN C 134 HIS D 89 GLN D 92 ASN D 338 ASN F 89 GLN F 134 HIS ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN G 326 ASN G 353 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.181750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.139550 restraints weight = 19312.962| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.42 r_work: 0.3346 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20167 Z= 0.137 Angle : 0.588 7.667 27377 Z= 0.285 Chirality : 0.039 0.128 3255 Planarity : 0.004 0.039 3178 Dihedral : 12.712 85.131 4522 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.40 % Allowed : 18.47 % Favored : 77.13 % 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: 1.41 (0.18), residues: 2380 helix: 2.15 (0.14), residues: 1540 sheet: -0.17 (0.56), residues: 91 loop : -1.61 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 254 TYR 0.012 0.001 TYR D 230 PHE 0.015 0.002 PHE C 54 TRP 0.030 0.002 TRP G 74 HIS 0.003 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00314 (20146) covalent geometry : angle 0.58567 (27328) SS BOND : bond 0.00293 ( 14) SS BOND : angle 0.70726 ( 28) hydrogen bonds : bond 0.03684 ( 1226) hydrogen bonds : angle 4.03174 ( 3531) link_NAG-ASN : bond 0.00546 ( 7) link_NAG-ASN : angle 1.97373 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 338 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7688 (tt0) cc_final: 0.7181 (mm-30) REVERT: A 65 SER cc_start: 0.8745 (m) cc_final: 0.8517 (p) REVERT: A 89 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8205 (mm-40) REVERT: A 100 ASN cc_start: 0.7701 (m-40) cc_final: 0.7378 (m-40) REVERT: A 135 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7010 (tt) REVERT: A 201 LYS cc_start: 0.6826 (tppp) cc_final: 0.6623 (tppt) REVERT: A 208 ASN cc_start: 0.6661 (t0) cc_final: 0.6452 (t0) REVERT: A 222 ILE cc_start: 0.8233 (mt) cc_final: 0.7972 (mt) REVERT: A 264 GLN cc_start: 0.8934 (tp40) cc_final: 0.8606 (mm-40) REVERT: A 343 LYS cc_start: 0.5901 (OUTLIER) cc_final: 0.5074 (mmtp) REVERT: B 70 SER cc_start: 0.8114 (p) cc_final: 0.7774 (m) REVERT: B 100 ASN cc_start: 0.7656 (m-40) cc_final: 0.6694 (t0) REVERT: B 222 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 254 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7412 (mtt-85) REVERT: B 262 GLN cc_start: 0.8555 (pt0) cc_final: 0.8322 (pt0) REVERT: C 9 GLU cc_start: 0.7864 (mt-10) cc_final: 0.6921 (mm-30) REVERT: C 35 ASP cc_start: 0.7493 (m-30) cc_final: 0.7042 (m-30) REVERT: C 100 ASN cc_start: 0.7883 (m-40) cc_final: 0.6785 (t0) REVERT: C 201 LYS cc_start: 0.7126 (tppp) cc_final: 0.6825 (tmmt) REVERT: C 254 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7590 (mtt-85) REVERT: C 296 PHE cc_start: 0.7612 (m-80) cc_final: 0.7299 (m-80) REVERT: C 299 PHE cc_start: 0.6514 (t80) cc_final: 0.5887 (t80) REVERT: C 353 ASN cc_start: 0.7737 (m-40) cc_final: 0.7445 (m110) REVERT: C 355 LYS cc_start: 0.6177 (mtpt) cc_final: 0.5292 (mmpt) REVERT: D 9 GLU cc_start: 0.7875 (tt0) cc_final: 0.7558 (mt-10) REVERT: D 89 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: D 100 ASN cc_start: 0.7845 (m-40) cc_final: 0.6949 (t0) REVERT: D 208 ASN cc_start: 0.6884 (t0) cc_final: 0.6605 (t0) REVERT: D 212 LYS cc_start: 0.7222 (mttt) cc_final: 0.6993 (mttp) REVERT: D 222 ILE cc_start: 0.8122 (mt) cc_final: 0.7889 (mt) REVERT: D 254 ARG cc_start: 0.7370 (ttm110) cc_final: 0.7107 (mtt-85) REVERT: D 264 GLN cc_start: 0.9032 (tp40) cc_final: 0.8643 (mm-40) REVERT: D 343 LYS cc_start: 0.5260 (OUTLIER) cc_final: 0.4856 (mmtm) REVERT: E 36 LYS cc_start: 0.7604 (ttmm) cc_final: 0.6914 (ttpt) REVERT: E 56 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7570 (mp10) REVERT: E 89 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8477 (mm-40) REVERT: E 100 ASN cc_start: 0.7673 (m-40) cc_final: 0.6666 (t0) REVERT: E 101 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8254 (tp) REVERT: E 122 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7779 (mp) REVERT: E 139 LEU cc_start: 0.6886 (tp) cc_final: 0.6527 (tp) REVERT: E 201 LYS cc_start: 0.7095 (tppp) cc_final: 0.6827 (tmmt) REVERT: E 222 ILE cc_start: 0.8069 (mm) cc_final: 0.7831 (mt) REVERT: E 262 GLN cc_start: 0.8650 (pt0) cc_final: 0.8435 (pt0) REVERT: E 343 LYS cc_start: 0.5947 (pttp) cc_final: 0.5566 (mmmt) REVERT: E 355 LYS cc_start: 0.6336 (mtpm) cc_final: 0.5812 (mtmp) REVERT: F 9 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6728 (mm-30) REVERT: F 31 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6479 (tp30) REVERT: F 36 LYS cc_start: 0.7718 (ttmt) cc_final: 0.7477 (ttmt) REVERT: F 56 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: F 100 ASN cc_start: 0.7940 (m-40) cc_final: 0.6940 (t0) REVERT: F 122 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7827 (mp) REVERT: F 201 LYS cc_start: 0.7168 (tppp) cc_final: 0.6951 (tmmt) REVERT: F 222 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7650 (mt) REVERT: F 254 ARG cc_start: 0.7324 (ttm110) cc_final: 0.7075 (mtt-85) REVERT: F 299 PHE cc_start: 0.6435 (t80) cc_final: 0.6162 (t80) REVERT: G 56 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: G 100 ASN cc_start: 0.7941 (m-40) cc_final: 0.6935 (t0) REVERT: G 122 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7748 (mp) REVERT: G 208 ASN cc_start: 0.6852 (t0) cc_final: 0.6396 (t0) REVERT: G 347 CYS cc_start: 0.7525 (m) cc_final: 0.7273 (m) outliers start: 81 outliers final: 17 residues processed: 396 average time/residue: 0.5834 time to fit residues: 262.6059 Evaluate side-chains 343 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 311 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 93 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 0.0270 chunk 220 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 338 ASN B 338 ASN C 338 ASN D 89 GLN D 264 GLN D 338 ASN E 353 ASN F 264 GLN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.185236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145198 restraints weight = 19115.388| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.29 r_work: 0.3355 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20167 Z= 0.130 Angle : 0.577 7.871 27377 Z= 0.281 Chirality : 0.039 0.178 3255 Planarity : 0.004 0.038 3178 Dihedral : 12.238 89.731 4522 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.64 % Allowed : 20.15 % Favored : 76.21 % 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: 1.57 (0.18), residues: 2380 helix: 2.21 (0.14), residues: 1547 sheet: -0.04 (0.59), residues: 91 loop : -1.45 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 254 TYR 0.013 0.001 TYR B 331 PHE 0.015 0.002 PHE C 54 TRP 0.036 0.002 TRP F 74 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00298 (20146) covalent geometry : angle 0.57485 (27328) SS BOND : bond 0.00285 ( 14) SS BOND : angle 0.65138 ( 28) hydrogen bonds : bond 0.03619 ( 1226) hydrogen bonds : angle 3.97840 ( 3531) link_NAG-ASN : bond 0.00521 ( 7) link_NAG-ASN : angle 1.89668 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 318 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7599 (tt0) cc_final: 0.7196 (mm-30) REVERT: A 57 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: A 89 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8177 (mm-40) REVERT: A 100 ASN cc_start: 0.7690 (m-40) cc_final: 0.7397 (m-40) REVERT: A 122 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7970 (mp) REVERT: A 135 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7131 (tt) REVERT: A 201 LYS cc_start: 0.6830 (tppp) cc_final: 0.6611 (tppt) REVERT: A 337 GLU cc_start: 0.7256 (tp30) cc_final: 0.6798 (tm-30) REVERT: A 338 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.6966 (m110) REVERT: A 343 LYS cc_start: 0.5633 (pptt) cc_final: 0.4780 (mmtp) REVERT: B 70 SER cc_start: 0.8082 (p) cc_final: 0.7784 (m) REVERT: B 100 ASN cc_start: 0.7635 (m-40) cc_final: 0.6736 (t0) REVERT: B 222 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7752 (mt) REVERT: B 262 GLN cc_start: 0.8541 (pt0) cc_final: 0.8319 (pt0) REVERT: B 307 LYS cc_start: 0.6967 (tptt) cc_final: 0.6721 (tppp) REVERT: B 331 TYR cc_start: 0.8081 (m-80) cc_final: 0.7810 (m-80) REVERT: C 9 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7060 (mm-30) REVERT: C 35 ASP cc_start: 0.7543 (m-30) cc_final: 0.7139 (m-30) REVERT: C 56 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: C 74 TRP cc_start: 0.8315 (t-100) cc_final: 0.8077 (t-100) REVERT: C 89 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7231 (mt0) REVERT: C 100 ASN cc_start: 0.7851 (m-40) cc_final: 0.6820 (t0) REVERT: C 143 MET cc_start: 0.6830 (mtp) cc_final: 0.6580 (mtt) REVERT: C 201 LYS cc_start: 0.7205 (tppp) cc_final: 0.6930 (tmmt) REVERT: C 296 PHE cc_start: 0.7655 (m-80) cc_final: 0.7330 (m-80) REVERT: C 299 PHE cc_start: 0.6416 (t80) cc_final: 0.5861 (t80) REVERT: C 353 ASN cc_start: 0.7730 (m-40) cc_final: 0.7518 (m110) REVERT: C 355 LYS cc_start: 0.6233 (mtpt) cc_final: 0.5268 (mmpt) REVERT: D 9 GLU cc_start: 0.7925 (tt0) cc_final: 0.7605 (mt-10) REVERT: D 100 ASN cc_start: 0.7792 (m-40) cc_final: 0.6969 (t0) REVERT: D 208 ASN cc_start: 0.6777 (t0) cc_final: 0.6383 (t0) REVERT: D 219 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7661 (mp) REVERT: D 222 ILE cc_start: 0.8105 (mt) cc_final: 0.7880 (mt) REVERT: D 343 LYS cc_start: 0.5425 (pmtt) cc_final: 0.5112 (mmmt) REVERT: E 56 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7132 (pp30) REVERT: E 100 ASN cc_start: 0.7778 (m-40) cc_final: 0.6786 (t0) REVERT: E 129 PHE cc_start: 0.8482 (m-80) cc_final: 0.8267 (m-80) REVERT: E 139 LEU cc_start: 0.7060 (tp) cc_final: 0.6692 (tp) REVERT: E 201 LYS cc_start: 0.7150 (tppp) cc_final: 0.6865 (tmmt) REVERT: E 222 ILE cc_start: 0.8118 (mm) cc_final: 0.7893 (mt) REVERT: E 254 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7416 (mtt-85) REVERT: E 262 GLN cc_start: 0.8627 (pt0) cc_final: 0.8422 (pt0) REVERT: E 343 LYS cc_start: 0.5853 (pttp) cc_final: 0.5429 (mptm) REVERT: E 355 LYS cc_start: 0.6466 (mtpm) cc_final: 0.6179 (mtmm) REVERT: F 5 GLN cc_start: 0.7697 (tp40) cc_final: 0.7208 (tt0) REVERT: F 9 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6721 (mm-30) REVERT: F 31 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6395 (tp30) REVERT: F 36 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7582 (ttmt) REVERT: F 56 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7250 (mt0) REVERT: F 94 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7365 (pp) REVERT: F 100 ASN cc_start: 0.7960 (m-40) cc_final: 0.7038 (t0) REVERT: F 122 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7887 (mp) REVERT: F 201 LYS cc_start: 0.7155 (tppp) cc_final: 0.6817 (tmtt) REVERT: F 214 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7769 (mm) REVERT: F 299 PHE cc_start: 0.6535 (t80) cc_final: 0.6229 (t80) REVERT: F 326 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.6786 (p0) REVERT: G 50 ILE cc_start: 0.8483 (mt) cc_final: 0.8262 (mm) REVERT: G 56 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: G 100 ASN cc_start: 0.7934 (m-40) cc_final: 0.6996 (t0) REVERT: G 208 ASN cc_start: 0.6781 (t0) cc_final: 0.6412 (t0) REVERT: G 222 ILE cc_start: 0.8021 (mt) cc_final: 0.7820 (mt) outliers start: 67 outliers final: 23 residues processed: 366 average time/residue: 0.5901 time to fit residues: 244.8852 Evaluate side-chains 343 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 304 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 56 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 6 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 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 338 ASN B 89 GLN B 134 HIS B 338 ASN C 262 GLN C 338 ASN D 89 GLN D 338 ASN E 89 GLN E 134 HIS E 353 ASN F 89 GLN G 264 GLN G 353 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.181964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.140823 restraints weight = 19156.889| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.32 r_work: 0.3331 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20167 Z= 0.157 Angle : 0.603 7.844 27377 Z= 0.293 Chirality : 0.040 0.135 3255 Planarity : 0.004 0.039 3178 Dihedral : 12.179 87.455 4522 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.78 % Allowed : 19.23 % Favored : 75.99 % 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: 1.56 (0.18), residues: 2380 helix: 2.19 (0.14), residues: 1547 sheet: 0.02 (0.61), residues: 91 loop : -1.42 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 254 TYR 0.012 0.002 TYR D 230 PHE 0.017 0.002 PHE F 141 TRP 0.034 0.003 TRP G 74 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00373 (20146) covalent geometry : angle 0.59993 (27328) SS BOND : bond 0.00382 ( 14) SS BOND : angle 0.83395 ( 28) hydrogen bonds : bond 0.03896 ( 1226) hydrogen bonds : angle 4.05026 ( 3531) link_NAG-ASN : bond 0.00494 ( 7) link_NAG-ASN : angle 1.99489 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 308 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7677 (tt0) cc_final: 0.7375 (mt-10) REVERT: A 89 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8282 (mm-40) REVERT: A 100 ASN cc_start: 0.7747 (m-40) cc_final: 0.7428 (m110) REVERT: A 122 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7999 (mp) REVERT: A 135 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7145 (tt) REVERT: A 201 LYS cc_start: 0.6884 (tppp) cc_final: 0.6392 (tmtt) REVERT: A 299 PHE cc_start: 0.6736 (t80) cc_final: 0.6082 (t80) REVERT: A 337 GLU cc_start: 0.7180 (tp30) cc_final: 0.6621 (tm-30) REVERT: A 338 ASN cc_start: 0.7292 (OUTLIER) cc_final: 0.6810 (m110) REVERT: A 343 LYS cc_start: 0.5684 (pptt) cc_final: 0.4818 (mmtp) REVERT: B 70 SER cc_start: 0.8054 (p) cc_final: 0.7722 (m) REVERT: B 100 ASN cc_start: 0.7765 (m-40) cc_final: 0.7022 (t0) REVERT: B 262 GLN cc_start: 0.8581 (pt0) cc_final: 0.8348 (pt0) REVERT: B 337 GLU cc_start: 0.7317 (tp30) cc_final: 0.6734 (tm-30) REVERT: B 338 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7379 (m110) REVERT: C 9 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7084 (mm-30) REVERT: C 35 ASP cc_start: 0.7656 (m-30) cc_final: 0.7127 (m-30) REVERT: C 56 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: C 100 ASN cc_start: 0.7963 (m-40) cc_final: 0.6891 (t0) REVERT: C 143 MET cc_start: 0.6860 (mtp) cc_final: 0.6608 (mtt) REVERT: C 201 LYS cc_start: 0.7138 (tppp) cc_final: 0.6847 (tmmt) REVERT: C 296 PHE cc_start: 0.7596 (m-80) cc_final: 0.7296 (m-80) REVERT: C 299 PHE cc_start: 0.6444 (t80) cc_final: 0.5896 (t80) REVERT: C 353 ASN cc_start: 0.7770 (m-40) cc_final: 0.7555 (m110) REVERT: C 355 LYS cc_start: 0.6213 (mtpt) cc_final: 0.5227 (mmpt) REVERT: D 100 ASN cc_start: 0.7837 (m-40) cc_final: 0.7008 (t0) REVERT: D 208 ASN cc_start: 0.6935 (t0) cc_final: 0.6601 (t0) REVERT: D 343 LYS cc_start: 0.5514 (OUTLIER) cc_final: 0.5215 (mmmt) REVERT: E 56 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: E 100 ASN cc_start: 0.7973 (m-40) cc_final: 0.6962 (t0) REVERT: E 129 PHE cc_start: 0.8495 (m-80) cc_final: 0.8276 (m-80) REVERT: E 139 LEU cc_start: 0.7078 (tp) cc_final: 0.6757 (tp) REVERT: E 201 LYS cc_start: 0.7152 (tppp) cc_final: 0.6862 (tmmt) REVERT: E 222 ILE cc_start: 0.8094 (mm) cc_final: 0.7847 (mt) REVERT: E 262 GLN cc_start: 0.8674 (pt0) cc_final: 0.8443 (pt0) REVERT: E 343 LYS cc_start: 0.5931 (pttp) cc_final: 0.5630 (mmmt) REVERT: E 355 LYS cc_start: 0.6417 (mtpm) cc_final: 0.5367 (mmpt) REVERT: F 5 GLN cc_start: 0.7710 (tp40) cc_final: 0.7181 (tt0) REVERT: F 9 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6672 (mm-30) REVERT: F 31 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6538 (tp30) REVERT: F 36 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7553 (ttmt) REVERT: F 56 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7361 (mt0) REVERT: F 57 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: F 81 ASP cc_start: 0.8340 (m-30) cc_final: 0.8100 (m-30) REVERT: F 94 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7361 (pp) REVERT: F 100 ASN cc_start: 0.8041 (m-40) cc_final: 0.7036 (t0) REVERT: F 122 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7870 (mp) REVERT: F 201 LYS cc_start: 0.7245 (tppp) cc_final: 0.7000 (tmmt) REVERT: F 299 PHE cc_start: 0.6609 (t80) cc_final: 0.6302 (t80) REVERT: F 326 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.6885 (p0) REVERT: G 56 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: G 89 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.6949 (mp10) REVERT: G 100 ASN cc_start: 0.7974 (m-40) cc_final: 0.7032 (t0) REVERT: G 208 ASN cc_start: 0.6883 (t0) cc_final: 0.6588 (t0) REVERT: G 326 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6942 (p0) outliers start: 88 outliers final: 32 residues processed: 376 average time/residue: 0.5673 time to fit residues: 243.3293 Evaluate side-chains 348 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 326 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 38 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 71 optimal weight: 7.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 338 ASN C 338 ASN D 89 GLN D 338 ASN E 89 GLN E 353 ASN F 338 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.179840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137380 restraints weight = 19255.856| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.38 r_work: 0.3308 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20167 Z= 0.161 Angle : 0.605 7.876 27377 Z= 0.295 Chirality : 0.040 0.142 3255 Planarity : 0.004 0.040 3178 Dihedral : 12.114 83.849 4522 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.45 % Allowed : 19.83 % Favored : 75.72 % 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: 1.54 (0.18), residues: 2380 helix: 2.14 (0.14), residues: 1547 sheet: 0.02 (0.61), residues: 91 loop : -1.34 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 254 TYR 0.015 0.002 TYR C 345 PHE 0.018 0.002 PHE F 141 TRP 0.038 0.003 TRP G 74 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00383 (20146) covalent geometry : angle 0.60256 (27328) SS BOND : bond 0.00353 ( 14) SS BOND : angle 0.82639 ( 28) hydrogen bonds : bond 0.03914 ( 1226) hydrogen bonds : angle 4.07468 ( 3531) link_NAG-ASN : bond 0.00474 ( 7) link_NAG-ASN : angle 2.03380 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 313 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7700 (tt0) cc_final: 0.7355 (mt-10) REVERT: A 56 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7294 (mt0) REVERT: A 89 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8274 (mm-40) REVERT: A 100 ASN cc_start: 0.7655 (m-40) cc_final: 0.7376 (m110) REVERT: A 122 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7930 (mp) REVERT: A 135 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7101 (tt) REVERT: A 201 LYS cc_start: 0.6839 (tppp) cc_final: 0.6596 (tppt) REVERT: A 337 GLU cc_start: 0.7184 (tp30) cc_final: 0.6597 (tm-30) REVERT: A 338 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.6815 (m110) REVERT: A 343 LYS cc_start: 0.5620 (OUTLIER) cc_final: 0.4845 (mmtp) REVERT: B 57 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: B 70 SER cc_start: 0.8099 (p) cc_final: 0.7702 (m) REVERT: B 100 ASN cc_start: 0.7773 (m-40) cc_final: 0.6962 (t0) REVERT: B 262 GLN cc_start: 0.8609 (pt0) cc_final: 0.8373 (pt0) REVERT: B 331 TYR cc_start: 0.8118 (m-80) cc_final: 0.7805 (m-80) REVERT: B 337 GLU cc_start: 0.7265 (tp30) cc_final: 0.6647 (tm-30) REVERT: B 338 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.6871 (m110) REVERT: C 9 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7013 (mm-30) REVERT: C 35 ASP cc_start: 0.7654 (m-30) cc_final: 0.7170 (m-30) REVERT: C 56 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: C 89 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: C 100 ASN cc_start: 0.7996 (m-40) cc_final: 0.6874 (t0) REVERT: C 143 MET cc_start: 0.6796 (mtp) cc_final: 0.6538 (mtt) REVERT: C 201 LYS cc_start: 0.7073 (tppp) cc_final: 0.6762 (tmmt) REVERT: C 296 PHE cc_start: 0.7533 (m-80) cc_final: 0.7243 (m-80) REVERT: C 353 ASN cc_start: 0.7713 (m-40) cc_final: 0.7492 (m110) REVERT: C 355 LYS cc_start: 0.6141 (mtpt) cc_final: 0.5181 (mmpt) REVERT: D 100 ASN cc_start: 0.7796 (m-40) cc_final: 0.6863 (t0) REVERT: D 208 ASN cc_start: 0.6935 (t0) cc_final: 0.6586 (t0) REVERT: D 343 LYS cc_start: 0.5425 (OUTLIER) cc_final: 0.5108 (mmmt) REVERT: E 36 LYS cc_start: 0.7641 (ttmt) cc_final: 0.6745 (ttpt) REVERT: E 56 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7379 (mt0) REVERT: E 88 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8147 (m) REVERT: E 100 ASN cc_start: 0.8087 (m-40) cc_final: 0.7560 (m-40) REVERT: E 129 PHE cc_start: 0.8501 (m-80) cc_final: 0.8280 (m-80) REVERT: E 139 LEU cc_start: 0.7034 (tp) cc_final: 0.6696 (tp) REVERT: E 201 LYS cc_start: 0.7067 (tppp) cc_final: 0.6760 (tmmt) REVERT: E 222 ILE cc_start: 0.8082 (mm) cc_final: 0.7878 (mt) REVERT: E 262 GLN cc_start: 0.8696 (pt0) cc_final: 0.8453 (pt0) REVERT: E 343 LYS cc_start: 0.6023 (pttp) cc_final: 0.5581 (mptm) REVERT: E 355 LYS cc_start: 0.6339 (mtpm) cc_final: 0.5849 (mtmp) REVERT: F 5 GLN cc_start: 0.7659 (tp40) cc_final: 0.7079 (tt0) REVERT: F 9 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6577 (mm-30) REVERT: F 31 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6454 (tp30) REVERT: F 36 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7496 (ttmt) REVERT: F 56 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: F 57 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: F 94 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7439 (pp) REVERT: F 100 ASN cc_start: 0.8085 (m-40) cc_final: 0.7187 (t0) REVERT: F 122 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7858 (mp) REVERT: F 201 LYS cc_start: 0.7166 (tppp) cc_final: 0.6805 (tmtt) REVERT: F 326 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.6818 (p0) REVERT: G 56 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: G 89 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: G 100 ASN cc_start: 0.7954 (m-40) cc_final: 0.7014 (t0) REVERT: G 208 ASN cc_start: 0.6825 (t0) cc_final: 0.6544 (t0) REVERT: G 326 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.6929 (p0) outliers start: 82 outliers final: 40 residues processed: 369 average time/residue: 0.5836 time to fit residues: 244.0543 Evaluate side-chains 366 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 306 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 326 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 52 optimal weight: 0.9990 chunk 137 optimal weight: 0.0040 chunk 193 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 332 ASN B 338 ASN C 338 ASN D 89 GLN D 338 ASN E 89 GLN E 353 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.185987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145540 restraints weight = 19106.531| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.24 r_work: 0.3379 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20167 Z= 0.133 Angle : 0.577 7.966 27377 Z= 0.283 Chirality : 0.039 0.148 3255 Planarity : 0.004 0.040 3178 Dihedral : 11.763 79.652 4522 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.24 % Allowed : 20.42 % Favored : 75.34 % 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: 1.63 (0.18), residues: 2380 helix: 2.19 (0.14), residues: 1547 sheet: -0.07 (0.61), residues: 91 loop : -1.25 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 217 TYR 0.017 0.001 TYR C 345 PHE 0.019 0.002 PHE F 141 TRP 0.029 0.003 TRP C 74 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00306 (20146) covalent geometry : angle 0.57505 (27328) SS BOND : bond 0.00301 ( 14) SS BOND : angle 0.74154 ( 28) hydrogen bonds : bond 0.03614 ( 1226) hydrogen bonds : angle 4.02056 ( 3531) link_NAG-ASN : bond 0.00484 ( 7) link_NAG-ASN : angle 1.87617 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 311 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7657 (tt0) cc_final: 0.7245 (mm-30) REVERT: A 57 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: A 89 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8198 (mm-40) REVERT: A 122 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7988 (mp) REVERT: A 135 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7093 (tt) REVERT: A 201 LYS cc_start: 0.6893 (tppp) cc_final: 0.6662 (tppt) REVERT: A 337 GLU cc_start: 0.7159 (tp30) cc_final: 0.6551 (tm-30) REVERT: A 338 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.6632 (m110) REVERT: A 343 LYS cc_start: 0.5582 (OUTLIER) cc_final: 0.4844 (mmtp) REVERT: B 70 SER cc_start: 0.8062 (p) cc_final: 0.7722 (m) REVERT: B 100 ASN cc_start: 0.7731 (m-40) cc_final: 0.6967 (t0) REVERT: B 262 GLN cc_start: 0.8542 (pt0) cc_final: 0.8329 (pt0) REVERT: B 337 GLU cc_start: 0.7140 (tp30) cc_final: 0.6683 (tt0) REVERT: B 338 ASN cc_start: 0.7187 (OUTLIER) cc_final: 0.6055 (t0) REVERT: C 9 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7061 (mm-30) REVERT: C 35 ASP cc_start: 0.7604 (m-30) cc_final: 0.7140 (m-30) REVERT: C 56 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: C 89 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7180 (mt0) REVERT: C 100 ASN cc_start: 0.7957 (m-40) cc_final: 0.6923 (t0) REVERT: C 143 MET cc_start: 0.6840 (mtp) cc_final: 0.6592 (mtt) REVERT: C 201 LYS cc_start: 0.7073 (tppp) cc_final: 0.6776 (tmmt) REVERT: C 296 PHE cc_start: 0.7668 (m-80) cc_final: 0.7341 (m-80) REVERT: C 337 GLU cc_start: 0.7366 (tp30) cc_final: 0.6786 (tm-30) REVERT: C 338 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.6972 (m110) REVERT: C 353 ASN cc_start: 0.7790 (m-40) cc_final: 0.7570 (m110) REVERT: C 355 LYS cc_start: 0.6159 (mtpt) cc_final: 0.5203 (mmpt) REVERT: D 9 GLU cc_start: 0.7905 (tt0) cc_final: 0.7472 (mt-10) REVERT: D 57 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: D 100 ASN cc_start: 0.7740 (m-40) cc_final: 0.6886 (t0) REVERT: D 208 ASN cc_start: 0.6925 (t0) cc_final: 0.6599 (t0) REVERT: E 56 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: E 88 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8066 (m) REVERT: E 100 ASN cc_start: 0.8019 (m-40) cc_final: 0.7492 (m-40) REVERT: E 139 LEU cc_start: 0.7040 (tp) cc_final: 0.6688 (tp) REVERT: E 201 LYS cc_start: 0.7066 (tppp) cc_final: 0.6770 (tmmt) REVERT: E 262 GLN cc_start: 0.8647 (pt0) cc_final: 0.8393 (pt0) REVERT: E 343 LYS cc_start: 0.5879 (pttp) cc_final: 0.5484 (mptm) REVERT: E 355 LYS cc_start: 0.6357 (mtpm) cc_final: 0.5850 (mtmp) REVERT: F 5 GLN cc_start: 0.7617 (tp40) cc_final: 0.7059 (tt0) REVERT: F 9 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6583 (mm-30) REVERT: F 31 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6373 (tp30) REVERT: F 36 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7611 (ttmt) REVERT: F 56 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7167 (mt0) REVERT: F 57 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: F 100 ASN cc_start: 0.7932 (m-40) cc_final: 0.7504 (m-40) REVERT: F 122 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7905 (mp) REVERT: F 201 LYS cc_start: 0.7170 (tppp) cc_final: 0.6827 (tmtt) REVERT: G 56 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7120 (mt0) REVERT: G 89 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.6861 (mp10) REVERT: G 100 ASN cc_start: 0.7872 (m-40) cc_final: 0.7021 (t0) REVERT: G 208 ASN cc_start: 0.6821 (t0) cc_final: 0.6545 (t0) REVERT: G 326 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.6929 (p0) outliers start: 78 outliers final: 35 residues processed: 363 average time/residue: 0.5636 time to fit residues: 232.9113 Evaluate side-chains 360 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 306 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 326 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 225 optimal weight: 1.9990 chunk 139 optimal weight: 0.0000 chunk 235 optimal weight: 0.1980 chunk 43 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 165 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 233 optimal weight: 5.9990 overall best weight: 0.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 264 GLN A 338 ASN B 338 ASN C 338 ASN D 338 ASN E 89 GLN E 353 ASN F 89 GLN F 338 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.189065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148067 restraints weight = 19079.049| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.28 r_work: 0.3457 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20167 Z= 0.111 Angle : 0.550 7.976 27377 Z= 0.271 Chirality : 0.038 0.160 3255 Planarity : 0.004 0.040 3178 Dihedral : 11.225 73.074 4522 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.04 % Allowed : 21.67 % Favored : 75.29 % 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: 1.78 (0.19), residues: 2380 helix: 2.31 (0.14), residues: 1547 sheet: -0.18 (0.61), residues: 91 loop : -1.16 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 254 TYR 0.016 0.001 TYR B 345 PHE 0.020 0.001 PHE F 141 TRP 0.033 0.003 TRP G 74 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00234 (20146) covalent geometry : angle 0.54808 (27328) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.60554 ( 28) hydrogen bonds : bond 0.03239 ( 1226) hydrogen bonds : angle 3.94219 ( 3531) link_NAG-ASN : bond 0.00480 ( 7) link_NAG-ASN : angle 1.71570 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 311 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7473 (tt0) cc_final: 0.7166 (mm-30) REVERT: A 57 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: A 122 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8000 (mp) REVERT: A 135 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7094 (tt) REVERT: A 201 LYS cc_start: 0.6871 (tppp) cc_final: 0.6368 (tmtt) REVERT: A 243 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 337 GLU cc_start: 0.7034 (tp30) cc_final: 0.6511 (tt0) REVERT: A 338 ASN cc_start: 0.6877 (OUTLIER) cc_final: 0.6160 (m-40) REVERT: A 343 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.4872 (mmtp) REVERT: B 70 SER cc_start: 0.8109 (p) cc_final: 0.7783 (m) REVERT: B 100 ASN cc_start: 0.7691 (m-40) cc_final: 0.6857 (t0) REVERT: B 262 GLN cc_start: 0.8435 (pt0) cc_final: 0.8186 (pt0) REVERT: B 264 GLN cc_start: 0.8654 (tp40) cc_final: 0.8396 (mm-40) REVERT: B 337 GLU cc_start: 0.7261 (tp30) cc_final: 0.6922 (tm-30) REVERT: B 338 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.6069 (t0) REVERT: C 9 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6926 (mm-30) REVERT: C 35 ASP cc_start: 0.7449 (m-30) cc_final: 0.6990 (m-30) REVERT: C 56 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: C 89 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7128 (mt0) REVERT: C 143 MET cc_start: 0.6895 (mtp) cc_final: 0.6680 (mtt) REVERT: C 201 LYS cc_start: 0.7122 (tppp) cc_final: 0.6840 (tmmt) REVERT: C 208 ASN cc_start: 0.6721 (t0) cc_final: 0.6501 (t0) REVERT: C 296 PHE cc_start: 0.7545 (m-80) cc_final: 0.7194 (m-80) REVERT: C 299 PHE cc_start: 0.6417 (t80) cc_final: 0.5816 (t80) REVERT: C 337 GLU cc_start: 0.7403 (tp30) cc_final: 0.6917 (tm-30) REVERT: C 338 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.5932 (t0) REVERT: C 353 ASN cc_start: 0.7859 (m-40) cc_final: 0.7612 (m110) REVERT: C 355 LYS cc_start: 0.6247 (mtpt) cc_final: 0.5289 (mmpt) REVERT: D 9 GLU cc_start: 0.7914 (tt0) cc_final: 0.7222 (mm-30) REVERT: D 57 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: D 100 ASN cc_start: 0.7603 (m-40) cc_final: 0.6738 (t0) REVERT: D 208 ASN cc_start: 0.6794 (t0) cc_final: 0.6443 (t0) REVERT: D 262 GLN cc_start: 0.8325 (pt0) cc_final: 0.8103 (pt0) REVERT: D 337 GLU cc_start: 0.7235 (tp30) cc_final: 0.6961 (tt0) REVERT: E 9 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6553 (mm-30) REVERT: E 56 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7335 (mt0) REVERT: E 139 LEU cc_start: 0.6997 (tp) cc_final: 0.6700 (tp) REVERT: E 201 LYS cc_start: 0.7086 (tppp) cc_final: 0.6794 (tmmt) REVERT: E 222 ILE cc_start: 0.8111 (mt) cc_final: 0.7860 (mt) REVERT: E 262 GLN cc_start: 0.8540 (pt0) cc_final: 0.8284 (pt0) REVERT: E 335 LEU cc_start: 0.7032 (mt) cc_final: 0.6782 (mt) REVERT: E 355 LYS cc_start: 0.6434 (mtpm) cc_final: 0.5918 (mtmp) REVERT: F 5 GLN cc_start: 0.7710 (tp40) cc_final: 0.7145 (tt0) REVERT: F 9 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6531 (mm-30) REVERT: F 31 GLU cc_start: 0.6930 (mt-10) cc_final: 0.5990 (tp30) REVERT: F 36 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7579 (ttmt) REVERT: F 56 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7123 (mt0) REVERT: F 57 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: F 100 ASN cc_start: 0.7892 (m-40) cc_final: 0.7472 (m-40) REVERT: F 201 LYS cc_start: 0.7203 (tppp) cc_final: 0.6864 (tmtt) REVERT: F 222 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7701 (mt) REVERT: F 337 GLU cc_start: 0.7303 (tp30) cc_final: 0.6933 (tm-30) REVERT: F 338 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6661 (m110) REVERT: G 56 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6855 (mt0) REVERT: G 100 ASN cc_start: 0.7727 (m-40) cc_final: 0.6902 (t0) REVERT: G 208 ASN cc_start: 0.6793 (t0) cc_final: 0.6509 (t0) REVERT: G 254 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7561 (mtt-85) REVERT: G 326 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.6885 (p0) outliers start: 56 outliers final: 17 residues processed: 349 average time/residue: 0.5439 time to fit residues: 215.8731 Evaluate side-chains 328 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 294 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 338 ASN Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 326 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 43 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN B 338 ASN C 338 ASN D 338 ASN E 89 GLN F 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.187096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.146992 restraints weight = 19056.659| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.23 r_work: 0.3407 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20167 Z= 0.137 Angle : 0.576 8.078 27377 Z= 0.283 Chirality : 0.039 0.149 3255 Planarity : 0.004 0.040 3178 Dihedral : 11.295 74.976 4522 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.34 % Allowed : 22.32 % Favored : 75.34 % 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: 1.75 (0.19), residues: 2380 helix: 2.28 (0.14), residues: 1547 sheet: -0.25 (0.60), residues: 91 loop : -1.14 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 254 TYR 0.015 0.001 TYR C 345 PHE 0.022 0.002 PHE F 141 TRP 0.038 0.003 TRP G 74 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00319 (20146) covalent geometry : angle 0.57359 (27328) SS BOND : bond 0.00304 ( 14) SS BOND : angle 0.68592 ( 28) hydrogen bonds : bond 0.03553 ( 1226) hydrogen bonds : angle 3.98594 ( 3531) link_NAG-ASN : bond 0.00420 ( 7) link_NAG-ASN : angle 1.81884 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7656 (tt0) cc_final: 0.7264 (mm-30) REVERT: A 57 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: A 122 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 135 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7146 (tt) REVERT: A 201 LYS cc_start: 0.6920 (tppp) cc_final: 0.6441 (tmtt) REVERT: A 243 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7830 (mt-10) REVERT: A 338 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7075 (m110) REVERT: A 339 ILE cc_start: 0.7409 (tp) cc_final: 0.7204 (tt) REVERT: A 343 LYS cc_start: 0.5624 (OUTLIER) cc_final: 0.4883 (mmtp) REVERT: B 70 SER cc_start: 0.8103 (p) cc_final: 0.7792 (m) REVERT: B 100 ASN cc_start: 0.7723 (m-40) cc_final: 0.6936 (t0) REVERT: B 262 GLN cc_start: 0.8493 (pt0) cc_final: 0.8267 (pt0) REVERT: B 331 TYR cc_start: 0.8222 (m-80) cc_final: 0.7984 (m-80) REVERT: B 335 LEU cc_start: 0.7018 (mt) cc_final: 0.6768 (mt) REVERT: B 337 GLU cc_start: 0.7321 (tp30) cc_final: 0.6889 (tm-30) REVERT: B 338 ASN cc_start: 0.6923 (OUTLIER) cc_final: 0.5858 (t0) REVERT: C 9 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7056 (mm-30) REVERT: C 35 ASP cc_start: 0.7642 (m-30) cc_final: 0.7234 (m-30) REVERT: C 89 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7099 (mt0) REVERT: C 143 MET cc_start: 0.6937 (mtp) cc_final: 0.6726 (mtt) REVERT: C 201 LYS cc_start: 0.7098 (tppp) cc_final: 0.6813 (tmmt) REVERT: C 296 PHE cc_start: 0.7639 (m-80) cc_final: 0.7283 (m-80) REVERT: C 337 GLU cc_start: 0.7358 (tp30) cc_final: 0.6805 (tm-30) REVERT: C 338 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.6605 (m110) REVERT: C 353 ASN cc_start: 0.7862 (m-40) cc_final: 0.7623 (m110) REVERT: D 9 GLU cc_start: 0.7939 (tt0) cc_final: 0.7539 (mt-10) REVERT: D 57 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: D 100 ASN cc_start: 0.7677 (m-40) cc_final: 0.6857 (t0) REVERT: D 208 ASN cc_start: 0.6862 (t0) cc_final: 0.6578 (t0) REVERT: D 212 LYS cc_start: 0.7450 (mttt) cc_final: 0.7068 (mtmm) REVERT: D 336 GLU cc_start: 0.7237 (tt0) cc_final: 0.6977 (mt-10) REVERT: E 56 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7389 (mt0) REVERT: E 139 LEU cc_start: 0.7088 (tp) cc_final: 0.6771 (tp) REVERT: E 201 LYS cc_start: 0.7120 (tppp) cc_final: 0.6844 (tmmt) REVERT: E 222 ILE cc_start: 0.8178 (mt) cc_final: 0.7917 (mt) REVERT: E 262 GLN cc_start: 0.8590 (pt0) cc_final: 0.8337 (pt0) REVERT: E 352 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6855 (tp30) REVERT: E 355 LYS cc_start: 0.6376 (mtpm) cc_final: 0.5856 (mtmp) REVERT: F 5 GLN cc_start: 0.7743 (tp40) cc_final: 0.7210 (tt0) REVERT: F 9 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6659 (mm-30) REVERT: F 31 GLU cc_start: 0.7099 (mt-10) cc_final: 0.5993 (tp30) REVERT: F 36 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7661 (ttmt) REVERT: F 56 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7259 (mt0) REVERT: F 57 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: F 100 ASN cc_start: 0.7918 (m-40) cc_final: 0.7528 (m-40) REVERT: F 201 LYS cc_start: 0.7246 (tppp) cc_final: 0.6911 (tmtt) REVERT: F 222 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7815 (mt) REVERT: F 337 GLU cc_start: 0.7353 (tp30) cc_final: 0.6988 (tm-30) REVERT: F 338 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.6812 (m110) REVERT: G 56 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: G 100 ASN cc_start: 0.7867 (m-40) cc_final: 0.7465 (m-40) REVERT: G 208 ASN cc_start: 0.6876 (t0) cc_final: 0.6607 (t0) REVERT: G 326 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7000 (p0) outliers start: 43 outliers final: 17 residues processed: 324 average time/residue: 0.5517 time to fit residues: 203.6810 Evaluate side-chains 323 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 290 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 338 ASN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 338 ASN Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 326 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 73 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.187053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146303 restraints weight = 19150.700| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.25 r_work: 0.3395 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20167 Z= 0.159 Angle : 0.813 59.200 27377 Z= 0.468 Chirality : 0.041 0.547 3255 Planarity : 0.006 0.154 3178 Dihedral : 11.305 74.992 4522 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.23 % Allowed : 22.16 % Favored : 75.61 % Cbeta Deviations : 0.13 % 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: 1.74 (0.19), residues: 2380 helix: 2.27 (0.14), residues: 1547 sheet: -0.29 (0.59), residues: 91 loop : -1.14 (0.25), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 254 TYR 0.013 0.001 TYR C 345 PHE 0.020 0.002 PHE F 141 TRP 0.038 0.003 TRP G 74 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00345 (20146) covalent geometry : angle 0.81218 (27328) SS BOND : bond 0.00308 ( 14) SS BOND : angle 0.67629 ( 28) hydrogen bonds : bond 0.03649 ( 1226) hydrogen bonds : angle 4.00405 ( 3531) link_NAG-ASN : bond 0.00418 ( 7) link_NAG-ASN : angle 1.82543 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7504.87 seconds wall clock time: 128 minutes 30.36 seconds (7710.36 seconds total)