Starting phenix.real_space_refine on Sun Sep 13 03:51:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wbf_21588/09_2026/6wbf_21588.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbf_21588/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wbf_21588/09_2026/6wbf_21588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbf_21588/09_2026/6wbf_21588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wbf_21588/09_2026/6wbf_21588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbf_21588/09_2026/6wbf_21588.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wbf_21588/09_2026/6wbf_21588.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wbf_21588/09_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-2.2.1-6174/lib/python3.11/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: 47 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: 47 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: 47 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: 47 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: 47 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: 47 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: 47 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.92, per 1000 atoms: 0.20 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: 1.75 Conformation dependent library (CDL) restraints added in 784.3 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: 0.56 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: 3.37 Time building geometry restraints manager: 2.30 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: 11289 29.69 - 59.39: 543 59.39 - 89.08: 32 89.08 - 118.77: 1 118.77 - 148.47: 14 Dihedral angle restraints: 11879 sinusoidal: 4704 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 11876 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: 0.07 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: 0.920 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.060 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 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 : 17.101 148.466 7175 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/Z covalent geometry : bond 0.00699 / 0.34 (20146) covalent geometry : angle 0.82613 / 0.46 (27328) SS BOND : bond 0.00264 / 0.17 ( 14) SS BOND : angle 0.72614 / 0.51 ( 28) hydrogen bonds : bond 0.14007 / 8.93 ( 1226) hydrogen bonds : angle 5.41394 / 3.85 ( 3531) link_NAG-ASN : bond 0.00610 / 0.41 ( 7) link_NAG-ASN : angle 0.87820 / 0.64 ( 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 : 0.876 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: 0.5522 time to fit residues: 328.7876 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 : 0.706 ------------------------------------------------------------------------------- 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... 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 = 0.4020 r_free = 0.4020 target = 0.184503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134196 restraints weight = 19379.412| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.60 r_work: 0.3357 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2229 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= 0.140 Angle : 0.636 8.836 27377 Z= 0.303 Chirality : 0.040 0.130 3255 Planarity : 0.004 0.040 3178 Dihedral : 15.277 125.303 3353 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.53 % Allowed : 14.56 % Favored : 81.91 % 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: 0.47 (0.18), residues: 2380 helix: 1.46 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.35 (0.20), 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/Z covalent geometry : bond 0.00319 / 0.14 (20146) covalent geometry : angle 0.63384 / 0.30 (27328) SS BOND : bond 0.00331 / 0.22 ( 14) SS BOND : angle 0.81491 / 0.58 ( 28) hydrogen bonds : bond 0.04045 / 2.64 ( 1226) hydrogen bonds : angle 4.09789 / 2.92 ( 3531) link_NAG-ASN : bond 0.00799 / 0.52 ( 7) link_NAG-ASN : angle 1.90604 / 1.31 ( 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: 65 poor density : 410 time to evaluate : 0.719 Fit side-chains REVERT: A 9 GLU cc_start: 0.7482 (tt0) cc_final: 0.6993 (mm-30) REVERT: A 65 SER cc_start: 0.9033 (m) cc_final: 0.8695 (p) REVERT: A 100 ASN cc_start: 0.7691 (m-40) cc_final: 0.6518 (t0) REVERT: A 201 LYS cc_start: 0.7012 (tppp) cc_final: 0.6790 (tppt) REVERT: A 208 ASN cc_start: 0.6406 (t0) cc_final: 0.6163 (t0) REVERT: A 212 LYS cc_start: 0.6721 (mttt) cc_final: 0.6343 (mttp) REVERT: A 348 LEU cc_start: 0.7228 (mt) cc_final: 0.6960 (mt) REVERT: B 9 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6700 (mm-30) REVERT: B 35 ASP cc_start: 0.7362 (m-30) cc_final: 0.6795 (m-30) REVERT: B 70 SER cc_start: 0.7855 (p) cc_final: 0.7616 (m) REVERT: B 75 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8338 (mmt90) REVERT: B 100 ASN cc_start: 0.7495 (m-40) cc_final: 0.6457 (t0) REVERT: B 129 PHE cc_start: 0.8427 (m-80) cc_final: 0.8183 (m-80) REVERT: B 201 LYS cc_start: 0.7040 (tppp) cc_final: 0.6839 (tppt) REVERT: B 262 GLN cc_start: 0.8621 (pt0) cc_final: 0.8399 (pt0) REVERT: C 9 GLU cc_start: 0.7683 (mt-10) cc_final: 0.6641 (mm-30) REVERT: C 35 ASP cc_start: 0.7258 (m-30) cc_final: 0.6628 (m-30) REVERT: C 100 ASN cc_start: 0.8048 (m-40) cc_final: 0.6819 (t0) REVERT: C 128 ARG cc_start: 0.8132 (ttp-170) cc_final: 0.7922 (tmm160) REVERT: C 201 LYS cc_start: 0.7064 (tppp) cc_final: 0.6736 (tmmt) REVERT: C 208 ASN cc_start: 0.6616 (t0) cc_final: 0.6161 (t0) REVERT: C 222 ILE cc_start: 0.7765 (mm) cc_final: 0.7535 (mt) REVERT: C 229 ILE cc_start: 0.8464 (mt) cc_final: 0.8118 (mm) REVERT: C 296 PHE cc_start: 0.7443 (m-80) cc_final: 0.7160 (m-80) REVERT: C 299 PHE cc_start: 0.6381 (t80) cc_final: 0.5747 (t80) REVERT: C 355 LYS cc_start: 0.5523 (mtpt) cc_final: 0.4800 (mmpt) REVERT: D 75 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8267 (mmt180) REVERT: D 100 ASN cc_start: 0.7939 (m-40) cc_final: 0.6842 (t0) REVERT: D 208 ASN cc_start: 0.6365 (t0) cc_final: 0.6037 (t0) REVERT: D 214 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7576 (mm) REVERT: D 219 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7253 (mp) REVERT: D 229 ILE cc_start: 0.8421 (mt) cc_final: 0.8188 (mm) REVERT: D 254 ARG cc_start: 0.7400 (ttm110) cc_final: 0.7102 (ttm-80) REVERT: D 262 GLN cc_start: 0.8486 (pt0) cc_final: 0.8258 (pt0) REVERT: D 355 LYS cc_start: 0.6304 (mtpp) cc_final: 0.5762 (mtmp) REVERT: E 36 LYS cc_start: 0.7322 (ttmm) cc_final: 0.6639 (ttpt) REVERT: E 65 SER cc_start: 0.8996 (m) cc_final: 0.8739 (p) REVERT: E 100 ASN cc_start: 0.8079 (m-40) cc_final: 0.6779 (t0) REVERT: E 139 LEU cc_start: 0.6588 (tp) cc_final: 0.6181 (tp) REVERT: E 201 LYS cc_start: 0.7034 (tppp) cc_final: 0.6746 (tmmt) REVERT: E 222 ILE cc_start: 0.8034 (mm) cc_final: 0.7773 (mt) REVERT: E 254 ARG cc_start: 0.7253 (ttm110) cc_final: 0.7018 (ttm-80) REVERT: E 262 GLN cc_start: 0.8607 (pt0) cc_final: 0.8393 (pt0) REVERT: E 307 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6606 (tppp) REVERT: E 343 LYS cc_start: 0.5810 (pttp) cc_final: 0.5294 (mmmt) REVERT: E 355 LYS cc_start: 0.6119 (mtpm) cc_final: 0.5706 (mtmp) REVERT: F 9 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6509 (mm-30) REVERT: F 31 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7235 (tt0) REVERT: F 36 LYS cc_start: 0.7419 (ttmt) cc_final: 0.7189 (ttmt) REVERT: F 100 ASN cc_start: 0.8151 (m-40) cc_final: 0.6828 (t0) REVERT: F 139 LEU cc_start: 0.6582 (tp) cc_final: 0.6312 (tp) REVERT: F 201 LYS cc_start: 0.6874 (tppp) cc_final: 0.6602 (tmmt) REVERT: F 222 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7606 (mp) REVERT: F 229 ILE cc_start: 0.8460 (mt) cc_final: 0.8202 (mm) REVERT: F 254 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6890 (mtt-85) REVERT: G 9 GLU cc_start: 0.7289 (tt0) cc_final: 0.6954 (mp0) REVERT: G 100 ASN cc_start: 0.8114 (m-40) cc_final: 0.6920 (t0) REVERT: G 139 LEU cc_start: 0.6508 (tp) cc_final: 0.6242 (tp) REVERT: G 222 ILE cc_start: 0.7727 (mm) cc_final: 0.7464 (mt) REVERT: G 254 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7215 (ttm-80) outliers start: 65 outliers final: 8 residues processed: 458 average time/residue: 0.5536 time to fit residues: 291.1209 Evaluate side-chains 346 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 334 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 294 THR 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: 8.9990 chunk 50 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 135 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 338 ASN B 338 ASN C 89 GLN C 338 ASN D 89 GLN D 92 ASN D 338 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.188302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148185 restraints weight = 19253.567| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.36 r_work: 0.3363 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20167 Z= 0.135 Angle : 0.595 7.521 27377 Z= 0.288 Chirality : 0.039 0.128 3255 Planarity : 0.004 0.038 3178 Dihedral : 12.521 98.036 3353 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.62 % Allowed : 16.73 % Favored : 78.65 % 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: 0.85 (0.18), residues: 2380 helix: 1.77 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.25 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 254 TYR 0.011 0.001 TYR C 230 PHE 0.013 0.001 PHE E 129 TRP 0.034 0.002 TRP G 74 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (20146) covalent geometry : angle 0.59270 / 0.29 (27328) SS BOND : bond 0.00301 / 0.20 ( 14) SS BOND : angle 0.69821 / 0.51 ( 28) hydrogen bonds : bond 0.03772 / 2.46 ( 1226) hydrogen bonds : angle 3.99502 / 2.84 ( 3531) link_NAG-ASN : bond 0.00551 / 0.36 ( 7) link_NAG-ASN : angle 1.79905 / 1.25 ( 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 441 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 356 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7544 (tt0) cc_final: 0.7187 (mm-30) REVERT: A 65 SER cc_start: 0.8767 (m) cc_final: 0.8537 (p) REVERT: A 100 ASN cc_start: 0.7704 (m-40) cc_final: 0.6818 (t0) REVERT: A 139 LEU cc_start: 0.7012 (tp) cc_final: 0.6570 (tp) REVERT: A 201 LYS cc_start: 0.7294 (tppp) cc_final: 0.6900 (tmtt) REVERT: A 204 LYS cc_start: 0.6869 (tttt) cc_final: 0.6660 (tttt) REVERT: A 207 ASN cc_start: 0.7275 (p0) cc_final: 0.7055 (p0) REVERT: A 208 ASN cc_start: 0.6681 (t0) cc_final: 0.6402 (t0) REVERT: A 348 LEU cc_start: 0.7577 (mt) cc_final: 0.7359 (mt) REVERT: B 9 GLU cc_start: 0.7706 (mt-10) cc_final: 0.6914 (mm-30) REVERT: B 70 SER cc_start: 0.7859 (p) cc_final: 0.7634 (m) REVERT: B 100 ASN cc_start: 0.7617 (m-40) cc_final: 0.6708 (t0) REVERT: B 222 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7625 (mt) REVERT: B 262 GLN cc_start: 0.8530 (pt0) cc_final: 0.8312 (pt0) REVERT: B 307 LYS cc_start: 0.7060 (tptt) cc_final: 0.6817 (tppp) REVERT: B 343 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5792 (mmmt) REVERT: C 9 GLU cc_start: 0.7781 (mt-10) cc_final: 0.6864 (mm-30) REVERT: C 35 ASP cc_start: 0.7503 (m-30) cc_final: 0.6958 (m-30) REVERT: C 81 ASP cc_start: 0.8532 (m-30) cc_final: 0.8287 (m-30) REVERT: C 100 ASN cc_start: 0.7827 (m-40) cc_final: 0.6826 (t0) REVERT: C 201 LYS cc_start: 0.7160 (tppp) cc_final: 0.6901 (tmmt) REVERT: C 222 ILE cc_start: 0.7917 (mm) cc_final: 0.7715 (mt) REVERT: C 296 PHE cc_start: 0.7618 (m-80) cc_final: 0.7331 (m-80) REVERT: C 300 ARG cc_start: 0.7686 (mtp180) cc_final: 0.7483 (ptm-80) REVERT: C 347 CYS cc_start: 0.7607 (m) cc_final: 0.7386 (m) REVERT: C 353 ASN cc_start: 0.7610 (m-40) cc_final: 0.7353 (m-40) REVERT: C 355 LYS cc_start: 0.5650 (mtpt) cc_final: 0.5046 (mmpt) REVERT: D 30 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7458 (mm) REVERT: D 100 ASN cc_start: 0.7900 (m-40) cc_final: 0.7017 (t0) REVERT: D 208 ASN cc_start: 0.6677 (t0) cc_final: 0.6379 (t0) REVERT: D 219 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7479 (mp) REVERT: D 254 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7128 (mtt-85) REVERT: D 262 GLN cc_start: 0.8415 (pt0) cc_final: 0.8186 (pt0) REVERT: D 338 ASN cc_start: 0.6798 (m-40) cc_final: 0.6536 (t0) REVERT: D 343 LYS cc_start: 0.5124 (pmtt) cc_final: 0.4510 (mppt) REVERT: D 352 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6537 (tt0) REVERT: D 355 LYS cc_start: 0.6618 (mtpp) cc_final: 0.6025 (mtmp) REVERT: E 36 LYS cc_start: 0.7557 (ttmm) cc_final: 0.6893 (ttpt) REVERT: E 100 ASN cc_start: 0.8020 (m-40) cc_final: 0.7484 (m-40) REVERT: E 139 LEU cc_start: 0.6891 (tp) cc_final: 0.6543 (tp) REVERT: E 201 LYS cc_start: 0.7131 (tppp) cc_final: 0.6893 (tmmt) REVERT: E 204 LYS cc_start: 0.7000 (tttt) cc_final: 0.6775 (tttt) REVERT: E 222 ILE cc_start: 0.8142 (mm) cc_final: 0.7823 (mt) REVERT: E 343 LYS cc_start: 0.5775 (pttp) cc_final: 0.5373 (mmmt) REVERT: E 355 LYS cc_start: 0.6309 (mtpm) cc_final: 0.5781 (mtmp) REVERT: F 9 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6754 (mm-30) REVERT: F 36 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7359 (ttmt) REVERT: F 56 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: F 100 ASN cc_start: 0.7889 (m-40) cc_final: 0.6838 (t0) REVERT: F 201 LYS cc_start: 0.7074 (tppp) cc_final: 0.6821 (tmmt) REVERT: F 222 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7683 (mp) REVERT: F 254 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7077 (mtt-85) REVERT: G 9 GLU cc_start: 0.7644 (tt0) cc_final: 0.7415 (mp0) REVERT: G 100 ASN cc_start: 0.7964 (m-40) cc_final: 0.6946 (t0) REVERT: G 222 ILE cc_start: 0.7858 (mm) cc_final: 0.7606 (mt) REVERT: G 307 LYS cc_start: 0.7060 (tptt) cc_final: 0.6838 (tppp) outliers start: 85 outliers final: 21 residues processed: 419 average time/residue: 0.5585 time to fit residues: 268.3718 Evaluate side-chains 351 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 294 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 56 GLN Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 219 LEU 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 338 ASN Chi-restraints excluded: chain F residue 56 GLN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 222 ILE 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 246 CYS Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 25 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 214 optimal weight: 0.5980 chunk 198 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 33 optimal weight: 0.0060 chunk 201 optimal weight: 5.9990 chunk 90 optimal weight: 0.0060 chunk 56 optimal weight: 1.9990 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 92 ASN A 338 ASN B 338 ASN C 134 HIS C 338 ASN D 89 GLN D 92 ASN E 89 GLN E 338 ASN E 353 ASN F 89 GLN F 338 ASN G 92 ASN G 264 GLN G 353 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.190237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149979 restraints weight = 19227.528| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.28 r_work: 0.3426 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20167 Z= 0.117 Angle : 0.557 7.577 27377 Z= 0.271 Chirality : 0.038 0.145 3255 Planarity : 0.004 0.038 3178 Dihedral : 11.731 95.680 3353 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.42 % Allowed : 19.12 % Favored : 77.46 % 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: 1.62 (0.18), residues: 2380 helix: 2.42 (0.14), residues: 1533 sheet: -0.60 (0.54), residues: 91 loop : -1.69 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 254 TYR 0.011 0.001 TYR G 331 PHE 0.013 0.001 PHE G 141 TRP 0.028 0.002 TRP G 74 HIS 0.002 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (20146) covalent geometry : angle 0.55507 / 0.27 (27328) SS BOND : bond 0.00309 / 0.21 ( 14) SS BOND : angle 0.63185 / 0.45 ( 28) hydrogen bonds : bond 0.03432 / 2.25 ( 1226) hydrogen bonds : angle 3.91677 / 2.79 ( 3531) link_NAG-ASN : bond 0.00728 / 0.44 ( 7) link_NAG-ASN : angle 1.78802 / 1.28 ( 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 394 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 331 time to evaluate : 0.710 Fit side-chains REVERT: A 9 GLU cc_start: 0.7421 (tt0) cc_final: 0.7209 (mm-30) REVERT: A 100 ASN cc_start: 0.7612 (m-40) cc_final: 0.6815 (t0) REVERT: A 122 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 139 LEU cc_start: 0.7026 (tp) cc_final: 0.6566 (tp) REVERT: A 201 LYS cc_start: 0.6790 (tppp) cc_final: 0.6359 (tmtt) REVERT: A 207 ASN cc_start: 0.7151 (p0) cc_final: 0.6949 (p0) REVERT: A 208 ASN cc_start: 0.6728 (t0) cc_final: 0.6248 (t0) REVERT: B 5 GLN cc_start: 0.7809 (tp40) cc_final: 0.7290 (tt0) REVERT: B 9 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6897 (mm-30) REVERT: B 70 SER cc_start: 0.7873 (p) cc_final: 0.7660 (m) REVERT: B 100 ASN cc_start: 0.7532 (m-40) cc_final: 0.6706 (t0) REVERT: B 222 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7628 (mt) REVERT: B 262 GLN cc_start: 0.8455 (pt0) cc_final: 0.8243 (pt0) REVERT: B 307 LYS cc_start: 0.7103 (tptt) cc_final: 0.6846 (tppp) REVERT: B 338 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6584 (t0) REVERT: C 9 GLU cc_start: 0.7721 (mt-10) cc_final: 0.6909 (mm-30) REVERT: C 35 ASP cc_start: 0.7440 (m-30) cc_final: 0.6988 (m-30) REVERT: C 100 ASN cc_start: 0.7785 (m-40) cc_final: 0.6800 (t0) REVERT: C 201 LYS cc_start: 0.7177 (tppp) cc_final: 0.6956 (tmmt) REVERT: C 204 LYS cc_start: 0.6813 (tttt) cc_final: 0.6571 (tttt) REVERT: C 296 PHE cc_start: 0.7709 (m-80) cc_final: 0.7367 (m-80) REVERT: C 353 ASN cc_start: 0.7653 (m-40) cc_final: 0.7397 (m110) REVERT: C 355 LYS cc_start: 0.6109 (mtpt) cc_final: 0.5127 (mmpt) REVERT: D 30 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7547 (mm) REVERT: D 100 ASN cc_start: 0.7760 (m-40) cc_final: 0.6942 (t0) REVERT: D 208 ASN cc_start: 0.6891 (t0) cc_final: 0.6335 (t0) REVERT: D 222 ILE cc_start: 0.8155 (mt) cc_final: 0.7893 (mp) REVERT: D 254 ARG cc_start: 0.7450 (ttm110) cc_final: 0.7212 (mtt-85) REVERT: D 262 GLN cc_start: 0.8348 (pt0) cc_final: 0.8108 (pt0) REVERT: D 264 GLN cc_start: 0.8845 (tp40) cc_final: 0.8457 (mm-40) REVERT: D 343 LYS cc_start: 0.5056 (pmtt) cc_final: 0.4852 (mmmt) REVERT: D 352 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6451 (tt0) REVERT: D 355 LYS cc_start: 0.6586 (mtpp) cc_final: 0.5897 (mtmp) REVERT: E 36 LYS cc_start: 0.7576 (ttmm) cc_final: 0.6916 (ttpt) REVERT: E 56 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6988 (pp30) REVERT: E 100 ASN cc_start: 0.7885 (m-40) cc_final: 0.6890 (t0) REVERT: E 139 LEU cc_start: 0.6860 (tp) cc_final: 0.6536 (tp) REVERT: E 201 LYS cc_start: 0.7123 (tppp) cc_final: 0.6882 (tmmt) REVERT: E 222 ILE cc_start: 0.8079 (mm) cc_final: 0.7765 (mt) REVERT: E 254 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7478 (mtt-85) REVERT: E 343 LYS cc_start: 0.5773 (pttp) cc_final: 0.5417 (mmmt) REVERT: E 355 LYS cc_start: 0.6477 (mtpm) cc_final: 0.6107 (mtmm) REVERT: F 9 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6756 (mm-30) REVERT: F 36 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7453 (ttmt) REVERT: F 100 ASN cc_start: 0.7790 (m-40) cc_final: 0.6828 (t0) REVERT: F 122 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7876 (mp) REVERT: F 201 LYS cc_start: 0.7039 (tppp) cc_final: 0.6777 (tmmt) REVERT: F 222 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7734 (mt) REVERT: F 254 ARG cc_start: 0.7335 (ttm110) cc_final: 0.7123 (mtt-85) REVERT: F 326 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6859 (p0) REVERT: G 100 ASN cc_start: 0.7891 (m-40) cc_final: 0.6919 (t0) REVERT: G 122 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7806 (mp) REVERT: G 208 ASN cc_start: 0.6731 (t0) cc_final: 0.6193 (t0) REVERT: G 222 ILE cc_start: 0.7883 (mm) cc_final: 0.7647 (mt) outliers start: 63 outliers final: 16 residues processed: 378 average time/residue: 0.5843 time to fit residues: 251.9764 Evaluate side-chains 335 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 310 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 343 LYS 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 91 LYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 240 LEU 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 F residue 326 ASN Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 122 LEU 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: 3.9990 chunk 112 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 134 HIS A 338 ASN B 326 ASN B 338 ASN C 262 GLN C 326 ASN C 338 ASN D 89 GLN D 326 ASN D 338 ASN E 134 HIS E 326 ASN E 338 ASN E 353 ASN F 89 GLN F 134 HIS F 326 ASN F 338 ASN G 326 ASN G 353 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.176119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.132511 restraints weight = 19326.366| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.48 r_work: 0.3236 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 20167 Z= 0.276 Angle : 0.740 7.934 27377 Z= 0.359 Chirality : 0.045 0.166 3255 Planarity : 0.005 0.041 3178 Dihedral : 12.999 87.248 3353 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.38 % Allowed : 18.14 % Favored : 76.48 % 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: 1.08 (0.18), residues: 2380 helix: 1.84 (0.13), residues: 1554 sheet: -0.20 (0.55), residues: 91 loop : -1.68 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 254 TYR 0.018 0.003 TYR G 10 PHE 0.025 0.003 PHE B 67 TRP 0.046 0.004 TRP G 74 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.28 (20146) covalent geometry : angle 0.73644 / 0.36 (27328) SS BOND : bond 0.00506 / 0.34 ( 14) SS BOND : angle 1.01871 / 0.72 ( 28) hydrogen bonds : bond 0.04874 / 3.19 ( 1226) hydrogen bonds : angle 4.37992 / 3.13 ( 3531) link_NAG-ASN : bond 0.00762 / 0.45 ( 7) link_NAG-ASN : angle 2.58973 / 1.82 ( 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 441 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 342 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7900 (tt0) cc_final: 0.7571 (mt-10) REVERT: A 65 SER cc_start: 0.8873 (m) cc_final: 0.8666 (p) REVERT: A 89 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: A 100 ASN cc_start: 0.7846 (m-40) cc_final: 0.7559 (m110) REVERT: A 122 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7901 (mp) REVERT: A 128 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: A 201 LYS cc_start: 0.6755 (tppp) cc_final: 0.6515 (tppt) REVERT: B 70 SER cc_start: 0.8136 (p) cc_final: 0.7719 (m) REVERT: B 89 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: B 100 ASN cc_start: 0.7841 (m-40) cc_final: 0.7052 (t0) REVERT: B 331 TYR cc_start: 0.8264 (m-80) cc_final: 0.8060 (m-80) REVERT: C 35 ASP cc_start: 0.7723 (m-30) cc_final: 0.7362 (m-30) REVERT: C 89 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: C 100 ASN cc_start: 0.8023 (m-40) cc_final: 0.6925 (t0) REVERT: C 201 LYS cc_start: 0.7323 (tppp) cc_final: 0.7057 (tmmt) REVERT: C 296 PHE cc_start: 0.7583 (m-80) cc_final: 0.7327 (m-80) REVERT: C 299 PHE cc_start: 0.6547 (t80) cc_final: 0.5970 (t80) REVERT: C 355 LYS cc_start: 0.5961 (mtpt) cc_final: 0.5079 (mmpt) REVERT: D 56 GLN cc_start: 0.7926 (tp-100) cc_final: 0.7243 (tt0) REVERT: D 100 ASN cc_start: 0.8005 (m-40) cc_final: 0.7050 (t0) REVERT: D 208 ASN cc_start: 0.7060 (t0) cc_final: 0.6731 (t0) REVERT: D 222 ILE cc_start: 0.8320 (mt) cc_final: 0.8050 (mt) REVERT: D 343 LYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5357 (mmtm) REVERT: E 36 LYS cc_start: 0.7636 (ttmm) cc_final: 0.6950 (ttpt) REVERT: E 89 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7405 (mm-40) REVERT: E 100 ASN cc_start: 0.8032 (m-40) cc_final: 0.6958 (t0) REVERT: E 139 LEU cc_start: 0.6972 (tp) cc_final: 0.6760 (tp) REVERT: E 143 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6296 (mmm) REVERT: E 201 LYS cc_start: 0.7003 (tppp) cc_final: 0.6515 (tmtm) REVERT: E 222 ILE cc_start: 0.8081 (mm) cc_final: 0.7869 (mt) REVERT: E 343 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5929 (mmmt) REVERT: E 355 LYS cc_start: 0.6361 (mtpm) cc_final: 0.5859 (mtmp) REVERT: F 36 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7505 (ttmt) REVERT: F 81 ASP cc_start: 0.8518 (m-30) cc_final: 0.8220 (m-30) REVERT: F 100 ASN cc_start: 0.8166 (m-40) cc_final: 0.7061 (t0) REVERT: F 122 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7870 (mp) REVERT: F 143 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.5321 (mmt) REVERT: F 148 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5733 (ttpt) REVERT: F 201 LYS cc_start: 0.7177 (tppp) cc_final: 0.6926 (tmmt) REVERT: F 222 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7708 (mt) REVERT: F 229 ILE cc_start: 0.8518 (mt) cc_final: 0.8265 (mm) REVERT: F 254 ARG cc_start: 0.7308 (ttm110) cc_final: 0.7064 (mtt-85) REVERT: F 294 THR cc_start: 0.8035 (m) cc_final: 0.7761 (p) REVERT: G 89 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: G 100 ASN cc_start: 0.8142 (m-40) cc_final: 0.7712 (m-40) REVERT: G 208 ASN cc_start: 0.6847 (t0) cc_final: 0.6593 (t0) REVERT: G 222 ILE cc_start: 0.7979 (mm) cc_final: 0.7764 (mt) outliers start: 99 outliers final: 34 residues processed: 400 average time/residue: 0.5542 time to fit residues: 253.6824 Evaluate side-chains 368 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 320 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 13 SER 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 128 ARG 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 B residue 3 ILE Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 246 CYS 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 68 SER 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 C residue 343 LYS 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 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 3 ILE Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 143 MET Chi-restraints excluded: chain F residue 148 LYS 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 89 GLN Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 6 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 178 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 338 ASN B 338 ASN C 338 ASN D 89 GLN D 338 ASN E 89 GLN E 338 ASN E 353 ASN F 264 GLN F 338 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.183596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142528 restraints weight = 19187.951| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.28 r_work: 0.3358 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3869 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= 0.133 Angle : 0.587 8.061 27377 Z= 0.288 Chirality : 0.039 0.140 3255 Planarity : 0.004 0.039 3178 Dihedral : 11.864 93.074 3353 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.69 % Allowed : 19.99 % Favored : 76.32 % 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: 1.48 (0.18), residues: 2380 helix: 2.16 (0.14), residues: 1540 sheet: -0.13 (0.59), residues: 91 loop : -1.48 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 217 TYR 0.012 0.001 TYR D 230 PHE 0.016 0.002 PHE C 54 TRP 0.039 0.003 TRP G 74 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (20146) covalent geometry : angle 0.58423 / 0.29 (27328) SS BOND : bond 0.00338 / 0.23 ( 14) SS BOND : angle 0.76398 / 0.54 ( 28) hydrogen bonds : bond 0.03665 / 2.40 ( 1226) hydrogen bonds : angle 4.06775 / 2.89 ( 3531) link_NAG-ASN : bond 0.00540 / 0.35 ( 7) link_NAG-ASN : angle 2.03045 / 1.40 ( 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 388 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 320 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7699 (tt0) cc_final: 0.7466 (mt-10) REVERT: A 100 ASN cc_start: 0.7701 (m-40) cc_final: 0.7411 (m-40) REVERT: A 122 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 201 LYS cc_start: 0.6823 (tppp) cc_final: 0.6609 (tppt) REVERT: A 337 GLU cc_start: 0.7278 (tp30) cc_final: 0.6649 (tm-30) REVERT: A 338 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7346 (m110) REVERT: A 343 LYS cc_start: 0.6077 (OUTLIER) cc_final: 0.5259 (mmtp) REVERT: B 70 SER cc_start: 0.8090 (p) cc_final: 0.7725 (m) REVERT: B 100 ASN cc_start: 0.7745 (m-40) cc_final: 0.6774 (t0) REVERT: B 122 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 262 GLN cc_start: 0.8586 (pt0) cc_final: 0.8348 (pt0) REVERT: B 331 TYR cc_start: 0.8230 (m-80) cc_final: 0.8001 (m-80) REVERT: C 35 ASP cc_start: 0.7506 (m-30) cc_final: 0.7038 (m-30) REVERT: C 100 ASN cc_start: 0.7911 (m-40) cc_final: 0.6854 (t0) REVERT: C 201 LYS cc_start: 0.7189 (tppp) cc_final: 0.6864 (tmmt) REVERT: C 296 PHE cc_start: 0.7648 (m-80) cc_final: 0.7302 (m-80) REVERT: C 299 PHE cc_start: 0.6424 (t80) cc_final: 0.5863 (t80) REVERT: C 353 ASN cc_start: 0.7676 (m-40) cc_final: 0.7457 (m110) REVERT: C 355 LYS cc_start: 0.6121 (mtpt) cc_final: 0.5216 (mmpt) REVERT: D 100 ASN cc_start: 0.7751 (m-40) cc_final: 0.6918 (t0) REVERT: D 208 ASN cc_start: 0.7075 (t0) cc_final: 0.6696 (t0) REVERT: D 222 ILE cc_start: 0.8299 (mt) cc_final: 0.8045 (mt) REVERT: D 254 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7427 (mtt-85) REVERT: D 264 GLN cc_start: 0.9024 (tp40) cc_final: 0.8594 (mm-40) REVERT: E 36 LYS cc_start: 0.7651 (ttmm) cc_final: 0.6982 (ttpt) REVERT: E 56 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7432 (mt0) REVERT: E 100 ASN cc_start: 0.7842 (m-40) cc_final: 0.6866 (t0) REVERT: E 129 PHE cc_start: 0.8507 (m-10) cc_final: 0.8295 (m-80) REVERT: E 139 LEU cc_start: 0.6913 (tp) cc_final: 0.6568 (tp) REVERT: E 201 LYS cc_start: 0.7078 (tppp) cc_final: 0.6759 (tmmt) REVERT: E 254 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7454 (mtt-85) REVERT: E 331 TYR cc_start: 0.8294 (m-80) cc_final: 0.8074 (m-80) REVERT: E 343 LYS cc_start: 0.5868 (pttp) cc_final: 0.5444 (mptm) REVERT: E 355 LYS cc_start: 0.6375 (mtpm) cc_final: 0.6096 (mtmm) REVERT: F 9 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6708 (mm-30) REVERT: F 36 LYS cc_start: 0.7747 (ttmt) cc_final: 0.7530 (ttmt) REVERT: F 100 ASN cc_start: 0.8031 (m-40) cc_final: 0.7070 (t0) REVERT: F 122 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7894 (mp) REVERT: F 201 LYS cc_start: 0.7164 (tppp) cc_final: 0.6888 (tmmt) REVERT: G 100 ASN cc_start: 0.8090 (m-40) cc_final: 0.7093 (t0) REVERT: G 148 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5736 (ttpt) REVERT: G 208 ASN cc_start: 0.6911 (t0) cc_final: 0.6602 (t0) outliers start: 68 outliers final: 25 residues processed: 365 average time/residue: 0.5711 time to fit residues: 238.2465 Evaluate side-chains 340 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain A residue 122 LEU 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 122 LEU 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 246 CYS Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 246 CYS 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 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 F residue 343 LYS Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 148 LYS Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR 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: 0.8980 chunk 14 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN A 338 ASN B 326 ASN B 338 ASN B 353 ASN C 338 ASN D 89 GLN D 326 ASN D 338 ASN E 89 GLN E 326 ASN E 338 ASN E 353 ASN F 326 ASN F 338 ASN G 332 ASN G 353 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.177014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133658 restraints weight = 19328.680| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.52 r_work: 0.3247 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20167 Z= 0.247 Angle : 0.707 8.220 27377 Z= 0.344 Chirality : 0.043 0.163 3255 Planarity : 0.005 0.042 3178 Dihedral : 12.795 88.132 3353 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.11 % Allowed : 19.50 % Favored : 75.39 % 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: 1.15 (0.18), residues: 2380 helix: 1.90 (0.14), residues: 1519 sheet: 0.07 (0.60), residues: 91 loop : -1.56 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 217 TYR 0.016 0.003 TYR B 10 PHE 0.022 0.002 PHE A 67 TRP 0.048 0.003 TRP G 74 HIS 0.005 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.25 (20146) covalent geometry : angle 0.70322 / 0.34 (27328) SS BOND : bond 0.00466 / 0.31 ( 14) SS BOND : angle 0.98232 / 0.70 ( 28) hydrogen bonds : bond 0.04663 / 3.07 ( 1226) hydrogen bonds : angle 4.29321 / 3.05 ( 3531) link_NAG-ASN : bond 0.00431 / 0.29 ( 7) link_NAG-ASN : angle 2.42914 / 1.70 ( 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 414 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 320 time to evaluate : 0.720 Fit side-chains REVERT: A 9 GLU cc_start: 0.7875 (tt0) cc_final: 0.7480 (mt-10) REVERT: A 30 LEU cc_start: 0.7942 (mt) cc_final: 0.7738 (mm) REVERT: A 56 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: A 100 ASN cc_start: 0.7867 (m-40) cc_final: 0.7567 (m110) REVERT: A 122 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 201 LYS cc_start: 0.6862 (tppp) cc_final: 0.6600 (tppt) REVERT: A 343 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5330 (mmtp) REVERT: B 57 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: B 70 SER cc_start: 0.8178 (p) cc_final: 0.7745 (m) REVERT: B 100 ASN cc_start: 0.7874 (m-40) cc_final: 0.7387 (m-40) REVERT: B 243 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 262 GLN cc_start: 0.8786 (pt0) cc_final: 0.8541 (pt0) REVERT: B 331 TYR cc_start: 0.8250 (m-80) cc_final: 0.7928 (m-80) REVERT: B 349 LYS cc_start: 0.6846 (mmtt) cc_final: 0.6527 (mmtt) REVERT: C 35 ASP cc_start: 0.7628 (m-30) cc_final: 0.7191 (m-30) REVERT: C 89 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7066 (mp10) REVERT: C 100 ASN cc_start: 0.8034 (m-40) cc_final: 0.7587 (m110) REVERT: C 201 LYS cc_start: 0.7143 (tppp) cc_final: 0.6838 (tmmt) REVERT: C 296 PHE cc_start: 0.7584 (m-80) cc_final: 0.7329 (m-80) REVERT: C 355 LYS cc_start: 0.6009 (mtpt) cc_final: 0.5066 (mmpt) REVERT: D 56 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7076 (pp30) REVERT: D 100 ASN cc_start: 0.7891 (m-40) cc_final: 0.6937 (t0) REVERT: D 208 ASN cc_start: 0.7103 (t0) cc_final: 0.6815 (t0) REVERT: D 222 ILE cc_start: 0.8383 (mt) cc_final: 0.8102 (mt) REVERT: D 254 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7496 (mtt-85) REVERT: E 36 LYS cc_start: 0.7671 (ttmm) cc_final: 0.6972 (ttpt) REVERT: E 100 ASN cc_start: 0.8112 (m-40) cc_final: 0.7582 (m-40) REVERT: E 129 PHE cc_start: 0.8576 (m-80) cc_final: 0.8331 (m-80) REVERT: E 139 LEU cc_start: 0.7084 (tp) cc_final: 0.6851 (tp) REVERT: E 143 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6329 (mmt) REVERT: E 201 LYS cc_start: 0.7068 (tppp) cc_final: 0.6770 (tmmt) REVERT: E 343 LYS cc_start: 0.6268 (pttp) cc_final: 0.5888 (mmmt) REVERT: E 355 LYS cc_start: 0.6363 (mtpm) cc_final: 0.5895 (mtmp) REVERT: F 36 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7507 (ttmt) REVERT: F 56 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: F 81 ASP cc_start: 0.8514 (m-30) cc_final: 0.8245 (m-30) REVERT: F 100 ASN cc_start: 0.8142 (m-40) cc_final: 0.7276 (t0) REVERT: F 122 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7820 (mp) REVERT: F 201 LYS cc_start: 0.7153 (tppp) cc_final: 0.6886 (tmmt) REVERT: F 222 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7678 (mt) REVERT: F 254 ARG cc_start: 0.7267 (ttm110) cc_final: 0.7038 (mtt-85) REVERT: F 294 THR cc_start: 0.8005 (m) cc_final: 0.7755 (p) REVERT: G 56 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: G 89 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.6749 (mp10) REVERT: G 100 ASN cc_start: 0.8149 (m-40) cc_final: 0.7086 (t0) outliers start: 94 outliers final: 36 residues processed: 380 average time/residue: 0.5589 time to fit residues: 242.6935 Evaluate side-chains 369 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 56 GLN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 LEU 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 343 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 5 GLN 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 343 LYS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 68 SER 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 C residue 343 LYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 143 MET 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 30 LEU Chi-restraints excluded: chain F residue 56 GLN 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 F residue 343 LYS Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 52 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN B 338 ASN C 338 ASN D 89 GLN D 338 ASN E 89 GLN E 338 ASN E 353 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.180683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138213 restraints weight = 19257.037| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.38 r_work: 0.3329 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4173 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= 0.140 Angle : 0.593 8.120 27377 Z= 0.292 Chirality : 0.039 0.147 3255 Planarity : 0.004 0.041 3178 Dihedral : 11.924 89.322 3353 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.80 % Allowed : 20.37 % Favored : 75.83 % 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: 1.52 (0.18), residues: 2380 helix: 2.12 (0.14), residues: 1540 sheet: -0.19 (0.61), residues: 91 loop : -1.28 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 254 TYR 0.016 0.001 TYR C 345 PHE 0.018 0.002 PHE A 141 TRP 0.041 0.003 TRP G 74 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (20146) covalent geometry : angle 0.59062 / 0.29 (27328) SS BOND : bond 0.00323 / 0.22 ( 14) SS BOND : angle 0.80724 / 0.57 ( 28) hydrogen bonds : bond 0.03753 / 2.47 ( 1226) hydrogen bonds : angle 4.05661 / 2.88 ( 3531) link_NAG-ASN : bond 0.00506 / 0.33 ( 7) link_NAG-ASN : angle 2.00999 / 1.38 ( 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 388 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 318 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7659 (tt0) cc_final: 0.7394 (mt-10) REVERT: A 56 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: A 100 ASN cc_start: 0.7697 (m-40) cc_final: 0.7406 (m110) REVERT: A 122 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7874 (mp) REVERT: A 201 LYS cc_start: 0.6811 (tppp) cc_final: 0.6574 (tppt) REVERT: A 337 GLU cc_start: 0.7221 (tp30) cc_final: 0.6636 (tm-30) REVERT: A 338 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7171 (m110) REVERT: A 343 LYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5254 (mmtp) REVERT: A 355 LYS cc_start: 0.5910 (ttpp) cc_final: 0.4978 (mtpt) REVERT: B 57 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: B 70 SER cc_start: 0.8111 (p) cc_final: 0.7701 (m) REVERT: B 100 ASN cc_start: 0.7969 (m-40) cc_final: 0.7055 (t0) REVERT: B 122 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7830 (mp) REVERT: B 262 GLN cc_start: 0.8654 (pt0) cc_final: 0.8386 (pt0) REVERT: B 331 TYR cc_start: 0.8150 (m-80) cc_final: 0.7941 (m-80) REVERT: B 349 LYS cc_start: 0.6760 (mmtt) cc_final: 0.6499 (mmtt) REVERT: C 35 ASP cc_start: 0.7573 (m-30) cc_final: 0.7231 (m-30) REVERT: C 100 ASN cc_start: 0.7954 (m-40) cc_final: 0.6838 (t0) REVERT: C 201 LYS cc_start: 0.7085 (tppp) cc_final: 0.6746 (tmmt) REVERT: C 296 PHE cc_start: 0.7665 (m-80) cc_final: 0.7338 (m-80) REVERT: C 355 LYS cc_start: 0.6122 (mtpt) cc_final: 0.5174 (mmpt) REVERT: D 100 ASN cc_start: 0.7849 (m-40) cc_final: 0.6928 (t0) REVERT: D 208 ASN cc_start: 0.6959 (t0) cc_final: 0.6615 (t0) REVERT: D 219 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7636 (mp) REVERT: D 222 ILE cc_start: 0.8297 (mt) cc_final: 0.7948 (mt) REVERT: D 254 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7455 (mtt-85) REVERT: D 264 GLN cc_start: 0.9076 (tp40) cc_final: 0.8626 (mm-40) REVERT: E 36 LYS cc_start: 0.7591 (ttmm) cc_final: 0.6883 (ttpt) REVERT: E 57 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: E 100 ASN cc_start: 0.8031 (m-40) cc_final: 0.7491 (m-40) REVERT: E 129 PHE cc_start: 0.8507 (m-80) cc_final: 0.8265 (m-80) REVERT: E 139 LEU cc_start: 0.6976 (tp) cc_final: 0.6640 (tp) REVERT: E 201 LYS cc_start: 0.7072 (tppp) cc_final: 0.6777 (tmmt) REVERT: E 343 LYS cc_start: 0.6017 (pttp) cc_final: 0.5559 (mptm) REVERT: E 355 LYS cc_start: 0.6304 (mtpm) cc_final: 0.5838 (mtmp) REVERT: F 9 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6516 (mm-30) REVERT: F 36 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7497 (ttmt) REVERT: F 56 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: F 100 ASN cc_start: 0.8049 (m-40) cc_final: 0.6920 (t0) REVERT: F 122 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7867 (mp) REVERT: F 142 ILE cc_start: 0.7095 (mt) cc_final: 0.6863 (mm) REVERT: F 201 LYS cc_start: 0.7154 (tppp) cc_final: 0.6855 (tmmt) REVERT: F 345 TYR cc_start: 0.7633 (t80) cc_final: 0.7407 (t80) REVERT: G 89 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: G 100 ASN cc_start: 0.8005 (m-40) cc_final: 0.7513 (m-40) outliers start: 70 outliers final: 33 residues processed: 359 average time/residue: 0.5825 time to fit residues: 238.8784 Evaluate side-chains 355 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 311 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 LEU 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 57 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 246 CYS 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 68 SER Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 57 GLU 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 E residue 338 ASN Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 56 GLN 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 F residue 343 LYS Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 225 optimal weight: 0.8980 chunk 139 optimal weight: 0.4980 chunk 235 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 5 optimal weight: 0.4980 chunk 201 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 233 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN B 332 ASN B 338 ASN C 338 ASN D 338 ASN E 89 GLN E 338 ASN F 89 GLN G 100 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 = 0.185870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.145522 restraints weight = 19040.385| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.22 r_work: 0.3385 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4265 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= 0.122 Angle : 0.563 8.082 27377 Z= 0.278 Chirality : 0.039 0.157 3255 Planarity : 0.004 0.040 3178 Dihedral : 11.276 88.452 3353 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.15 % Allowed : 21.02 % Favored : 75.83 % 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: 1.64 (0.18), residues: 2380 helix: 2.27 (0.14), residues: 1512 sheet: -0.42 (0.60), residues: 91 loop : -1.19 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 254 TYR 0.014 0.001 TYR C 345 PHE 0.020 0.002 PHE F 141 TRP 0.041 0.002 TRP G 74 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (20146) covalent geometry : angle 0.56132 / 0.28 (27328) SS BOND : bond 0.00267 / 0.18 ( 14) SS BOND : angle 0.66218 / 0.48 ( 28) hydrogen bonds : bond 0.03492 / 2.30 ( 1226) hydrogen bonds : angle 3.95991 / 2.81 ( 3531) link_NAG-ASN : bond 0.00495 / 0.33 ( 7) link_NAG-ASN : angle 1.82543 / 1.24 ( 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 364 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 306 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7599 (tt0) cc_final: 0.7189 (mm-30) REVERT: A 56 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: A 100 ASN cc_start: 0.7590 (m-40) cc_final: 0.7351 (m110) REVERT: A 122 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7955 (mp) REVERT: A 201 LYS cc_start: 0.6870 (tppp) cc_final: 0.6360 (tmtt) REVERT: A 243 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 337 GLU cc_start: 0.7198 (tp30) cc_final: 0.6567 (tt0) REVERT: A 338 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6811 (m110) REVERT: A 343 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5265 (mmtp) REVERT: B 30 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7261 (mm) REVERT: B 57 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: B 70 SER cc_start: 0.8033 (p) cc_final: 0.7702 (m) REVERT: B 100 ASN cc_start: 0.7883 (m-40) cc_final: 0.7051 (t0) REVERT: B 262 GLN cc_start: 0.8555 (pt0) cc_final: 0.8269 (pt0) REVERT: B 337 GLU cc_start: 0.7293 (tp30) cc_final: 0.6736 (tm-30) REVERT: B 338 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6476 (m110) REVERT: B 349 LYS cc_start: 0.6813 (mmtt) cc_final: 0.6601 (mmtt) REVERT: C 9 GLU cc_start: 0.7800 (mt-10) cc_final: 0.6926 (mm-30) REVERT: C 35 ASP cc_start: 0.7546 (m-30) cc_final: 0.7167 (m-30) REVERT: C 143 MET cc_start: 0.6837 (mtp) cc_final: 0.6555 (mtt) REVERT: C 201 LYS cc_start: 0.7086 (tppp) cc_final: 0.6775 (tmmt) REVERT: C 208 ASN cc_start: 0.6726 (t0) cc_final: 0.6411 (t0) REVERT: C 296 PHE cc_start: 0.7567 (m-80) cc_final: 0.7192 (m-80) REVERT: C 355 LYS cc_start: 0.6152 (mtpt) cc_final: 0.5209 (mmpt) REVERT: D 100 ASN cc_start: 0.7779 (m-40) cc_final: 0.6943 (t0) REVERT: D 208 ASN cc_start: 0.7077 (t0) cc_final: 0.6719 (t0) REVERT: D 219 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7711 (mp) REVERT: D 222 ILE cc_start: 0.8285 (mt) cc_final: 0.7959 (mt) REVERT: D 264 GLN cc_start: 0.8951 (tp40) cc_final: 0.8546 (mm-40) REVERT: E 36 LYS cc_start: 0.7634 (ttmm) cc_final: 0.6943 (ttpt) REVERT: E 56 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: E 129 PHE cc_start: 0.8498 (m-80) cc_final: 0.8275 (m-80) REVERT: E 139 LEU cc_start: 0.6850 (tp) cc_final: 0.6494 (tp) REVERT: E 201 LYS cc_start: 0.7080 (tppp) cc_final: 0.6772 (tmmt) REVERT: E 254 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7397 (mtt-85) REVERT: E 355 LYS cc_start: 0.6369 (mtpm) cc_final: 0.5883 (mtmp) REVERT: F 5 GLN cc_start: 0.7677 (tp40) cc_final: 0.7143 (tt0) REVERT: F 9 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6509 (mm-30) REVERT: F 36 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7507 (ttmt) REVERT: F 100 ASN cc_start: 0.7928 (m-40) cc_final: 0.7547 (m-40) REVERT: F 122 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7879 (mp) REVERT: F 142 ILE cc_start: 0.7161 (mt) cc_final: 0.6943 (OUTLIER) REVERT: F 201 LYS cc_start: 0.7163 (tppp) cc_final: 0.6885 (tmmt) REVERT: F 345 TYR cc_start: 0.7604 (t80) cc_final: 0.7377 (t80) REVERT: G 100 ASN cc_start: 0.8012 (m110) cc_final: 0.7648 (m-40) outliers start: 58 outliers final: 23 residues processed: 345 average time/residue: 0.5726 time to fit residues: 226.1749 Evaluate side-chains 327 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 56 GLN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 LEU 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 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 C residue 3 ILE Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 343 LYS 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 F residue 101 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 258 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 43 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 137 optimal weight: 0.0270 chunk 124 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN B 338 ASN C 338 ASN D 89 GLN D 338 ASN E 89 GLN E 338 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.184227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.143549 restraints weight = 19131.035| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.24 r_work: 0.3360 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20167 Z= 0.133 Angle : 0.575 8.071 27377 Z= 0.285 Chirality : 0.039 0.151 3255 Planarity : 0.004 0.042 3178 Dihedral : 11.172 89.941 3353 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.72 % Allowed : 21.94 % 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: 1.64 (0.18), residues: 2380 helix: 2.27 (0.14), residues: 1512 sheet: -0.47 (0.61), residues: 91 loop : -1.17 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 254 TYR 0.014 0.001 TYR G 345 PHE 0.021 0.002 PHE F 141 TRP 0.044 0.003 TRP G 74 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (20146) covalent geometry : angle 0.57292 / 0.28 (27328) SS BOND : bond 0.00303 / 0.21 ( 14) SS BOND : angle 0.74264 / 0.53 ( 28) hydrogen bonds : bond 0.03585 / 2.35 ( 1226) hydrogen bonds : angle 3.96695 / 2.81 ( 3531) link_NAG-ASN : bond 0.00461 / 0.30 ( 7) link_NAG-ASN : angle 1.88423 / 1.28 ( 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 342 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 292 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7572 (tt0) cc_final: 0.7098 (mm-30) REVERT: A 56 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: A 57 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: A 100 ASN cc_start: 0.7587 (m-40) cc_final: 0.7337 (m110) REVERT: A 122 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 201 LYS cc_start: 0.6842 (tppp) cc_final: 0.6325 (tmtt) REVERT: A 337 GLU cc_start: 0.7244 (tp30) cc_final: 0.6676 (tm-30) REVERT: A 338 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7070 (m110) REVERT: A 343 LYS cc_start: 0.5854 (OUTLIER) cc_final: 0.5165 (mmtp) REVERT: B 57 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: B 70 SER cc_start: 0.8038 (p) cc_final: 0.7682 (m) REVERT: B 100 ASN cc_start: 0.7903 (m-40) cc_final: 0.7015 (t0) REVERT: B 262 GLN cc_start: 0.8579 (pt0) cc_final: 0.8288 (pt0) REVERT: B 337 GLU cc_start: 0.7233 (tp30) cc_final: 0.6643 (tt0) REVERT: B 338 ASN cc_start: 0.7330 (OUTLIER) cc_final: 0.6450 (m110) REVERT: C 9 GLU cc_start: 0.7844 (mt-10) cc_final: 0.6895 (mm-30) REVERT: C 35 ASP cc_start: 0.7504 (m-30) cc_final: 0.7105 (m-30) REVERT: C 143 MET cc_start: 0.6808 (mtp) cc_final: 0.6521 (mtt) REVERT: C 201 LYS cc_start: 0.7026 (tppp) cc_final: 0.6695 (tmmt) REVERT: C 208 ASN cc_start: 0.6689 (t0) cc_final: 0.6375 (t0) REVERT: C 296 PHE cc_start: 0.7508 (m-80) cc_final: 0.7174 (m-80) REVERT: C 355 LYS cc_start: 0.6128 (mtpt) cc_final: 0.5209 (mmpt) REVERT: D 100 ASN cc_start: 0.7813 (m-40) cc_final: 0.6909 (t0) REVERT: D 208 ASN cc_start: 0.7013 (t0) cc_final: 0.6612 (t0) REVERT: D 219 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7670 (mp) REVERT: D 222 ILE cc_start: 0.8286 (mt) cc_final: 0.7955 (mt) REVERT: D 264 GLN cc_start: 0.9011 (tp40) cc_final: 0.8615 (mm-40) REVERT: E 36 LYS cc_start: 0.7580 (ttmm) cc_final: 0.6868 (ttpt) REVERT: E 56 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: E 129 PHE cc_start: 0.8498 (m-80) cc_final: 0.8263 (m-80) REVERT: E 139 LEU cc_start: 0.6958 (tp) cc_final: 0.6654 (tp) REVERT: E 201 LYS cc_start: 0.7023 (tppp) cc_final: 0.6712 (tmmt) REVERT: E 254 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7365 (mtt-85) REVERT: E 355 LYS cc_start: 0.6324 (mtpm) cc_final: 0.5843 (mtmp) REVERT: F 5 GLN cc_start: 0.7587 (tp40) cc_final: 0.7050 (tt0) REVERT: F 9 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6408 (mm-30) REVERT: F 36 LYS cc_start: 0.7668 (ttmt) cc_final: 0.7444 (ttmt) REVERT: F 56 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7213 (mt0) REVERT: F 100 ASN cc_start: 0.7967 (m-40) cc_final: 0.7548 (m-40) REVERT: F 122 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7829 (mp) REVERT: F 201 LYS cc_start: 0.7121 (tppp) cc_final: 0.6839 (tmmt) REVERT: F 345 TYR cc_start: 0.7605 (t80) cc_final: 0.7368 (t80) REVERT: G 100 ASN cc_start: 0.8055 (m110) cc_final: 0.7592 (m-40) outliers start: 50 outliers final: 27 residues processed: 323 average time/residue: 0.5683 time to fit residues: 210.0471 Evaluate side-chains 326 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 56 GLN Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 LEU 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 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 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 246 CYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 219 LEU 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 101 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 338 ASN Chi-restraints excluded: chain F residue 56 GLN 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 9 GLU Chi-restraints excluded: chain G residue 258 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 73 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 31 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 108 optimal weight: 0.2980 chunk 159 optimal weight: 0.7980 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 338 ASN B 338 ASN C 338 ASN D 89 GLN D 264 GLN D 338 ASN E 89 GLN E 338 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.187271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.146829 restraints weight = 19108.056| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.23 r_work: 0.3410 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4340 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= 0.124 Angle : 0.565 8.051 27377 Z= 0.279 Chirality : 0.038 0.158 3255 Planarity : 0.004 0.040 3178 Dihedral : 10.931 89.850 3353 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.72 % Allowed : 21.94 % 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: 1.67 (0.18), residues: 2380 helix: 2.29 (0.14), residues: 1512 sheet: -0.56 (0.60), residues: 91 loop : -1.13 (0.24), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 128 TYR 0.016 0.001 TYR G 345 PHE 0.021 0.002 PHE F 141 TRP 0.043 0.003 TRP G 74 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (20146) covalent geometry : angle 0.56259 / 0.28 (27328) SS BOND : bond 0.00289 / 0.20 ( 14) SS BOND : angle 0.73349 / 0.52 ( 28) hydrogen bonds : bond 0.03486 / 2.29 ( 1226) hydrogen bonds : angle 3.94717 / 2.80 ( 3531) link_NAG-ASN : bond 0.00467 / 0.31 ( 7) link_NAG-ASN : angle 1.82918 / 1.24 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7564.74 seconds wall clock time: 129 minutes 51.46 seconds (7791.46 seconds total)