Starting phenix.real_space_refine on Thu Mar 5 08:06:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wbg_21589/03_2026/6wbg_21589.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbg_21589/03_2026/6wbg_21589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wbg_21589/03_2026/6wbg_21589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbg_21589/03_2026/6wbg_21589.map" model { file = "/net/cci-nas-00/data/ceres_data/6wbg_21589/03_2026/6wbg_21589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbg_21589/03_2026/6wbg_21589.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 21 5.49 5 S 77 5.16 5 C 13321 2.51 5 N 2912 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "F" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.70, per 1000 atoms: 0.24 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: 1.73 Conformation dependent library (CDL) restraints added in 901.8 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: 0.59 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: 3.630A 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: 3.949A 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: 3.619A 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: 3.830A 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: 3.681A 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: 3.630A 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: 3.947A 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: 3.718A 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: 3.682A 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: 3.629A 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: 3.620A 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: 3.718A 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: 4.014A 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: 3.681A 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: 4.014A 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: 3.682A 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: 3.629A 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: 3.949A 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: 3.718A 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: 3.717A 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: 4.014A 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: 3.632A 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: 3.949A 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: 3.717A 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: 4.013A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.830A 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: 3.682A 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: 3.38 Time building geometry restraints manager: 2.26 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: 2908 1.32 - 1.44: 5034 1.44 - 1.57: 12071 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 -0.035 1.17e-02 7.31e+03 9.16e+00 bond pdb=" N ASN B 369 " pdb=" CA ASN B 369 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.17e-02 7.31e+03 8.74e+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 8.65e+00 bond pdb=" N ASN D 369 " pdb=" CA ASN D 369 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.17e-02 7.31e+03 8.54e+00 bond pdb=" N ASN C 369 " pdb=" CA ASN C 369 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.17e-02 7.31e+03 8.49e+00 ... (remaining 20141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 26497 2.02 - 4.04: 712 4.04 - 6.06: 91 6.06 - 8.08: 14 8.08 - 10.10: 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 122.77 118.81 3.96 1.05e+00 9.07e-01 1.42e+01 angle pdb=" C TYR F 10 " pdb=" N VAL F 11 " pdb=" CA VAL F 11 " ideal model delta sigma weight residual 122.77 118.88 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 122.77 118.89 3.88 1.05e+00 9.07e-01 1.37e+01 angle pdb=" C TYR A 10 " pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 122.77 118.91 3.86 1.05e+00 9.07e-01 1.35e+01 angle pdb=" C TYR B 10 " pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 122.77 118.92 3.85 1.05e+00 9.07e-01 1.35e+01 ... (remaining 27323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.68: 12375 29.68 - 59.37: 626 59.37 - 89.05: 32 89.05 - 118.73: 1 118.73 - 148.41: 14 Dihedral angle restraints: 13048 sinusoidal: 5873 harmonic: 7175 Sorted by residual: dihedral pdb=" N1 PTY A 401 " pdb=" C2 PTY A 401 " pdb=" C3 PTY A 401 " pdb=" O11 PTY A 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.08 148.41 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" N1 PTY E 401 " pdb=" C2 PTY E 401 " pdb=" C3 PTY E 401 " pdb=" O11 PTY E 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.07 148.40 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 -83.06 148.39 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 13045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2266 0.039 - 0.077: 709 0.077 - 0.116: 223 0.116 - 0.154: 43 0.154 - 0.193: 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 2.63 -0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA ILE C 373 " pdb=" N ILE C 373 " pdb=" C ILE C 373 " pdb=" CB ILE C 373 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 3252 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 407 " 0.090 2.00e-02 2.50e+03 7.42e-02 6.88e+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 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 407 " -0.090 2.00e-02 2.50e+03 7.39e-02 6.83e+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 B 407 " -0.090 2.00e-02 2.50e+03 7.38e-02 6.81e+01 pdb=" C7 NAG B 407 " 0.026 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: 1406 2.73 - 3.27: 20895 3.27 - 3.81: 33193 3.81 - 4.36: 39549 4.36 - 4.90: 68923 Nonbonded interactions: 163966 Sorted by model distance: nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.183 3.040 nonbonded pdb=" O LEU A 52 " pdb=" OH TYR G 111 " 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 163961 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.230 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.827 10.103 27377 Z= 0.458 Chirality : 0.043 0.193 3255 Planarity : 0.005 0.074 3178 Dihedral : 16.592 148.414 8344 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.38 % Allowed : 5.76 % Favored : 93.86 % 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 (0.16), residues: 2380 helix: -0.10 (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 D 10 PHE 0.013 0.002 PHE B 54 TRP 0.008 0.001 TRP F 104 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00699 (20146) covalent geometry : angle 0.82747 (27328) SS BOND : bond 0.00249 ( 14) SS BOND : angle 0.73140 ( 28) hydrogen bonds : bond 0.14035 ( 1226) hydrogen bonds : angle 5.43804 ( 3531) link_NAG-ASN : bond 0.00607 ( 7) link_NAG-ASN : angle 0.88914 ( 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 213 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.711 Fit side-chains REVERT: A 29 ARG cc_start: 0.8631 (mpt-90) cc_final: 0.8279 (mmt90) REVERT: A 135 ILE cc_start: 0.9204 (tt) cc_final: 0.8958 (tp) REVERT: A 242 ASP cc_start: 0.8957 (p0) cc_final: 0.8716 (p0) REVERT: B 135 ILE cc_start: 0.9104 (tt) cc_final: 0.8874 (tp) REVERT: B 352 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8706 (tp30) REVERT: C 135 ILE cc_start: 0.9062 (tt) cc_final: 0.8860 (tp) REVERT: D 29 ARG cc_start: 0.8571 (mpt-90) cc_final: 0.8326 (mmt90) REVERT: D 135 ILE cc_start: 0.9094 (tt) cc_final: 0.8880 (tp) REVERT: F 135 ILE cc_start: 0.9058 (tt) cc_final: 0.8820 (tp) REVERT: G 29 ARG cc_start: 0.8571 (mpt-90) cc_final: 0.8351 (mmt90) REVERT: G 135 ILE cc_start: 0.9075 (tt) cc_final: 0.8838 (tp) outliers start: 7 outliers final: 0 residues processed: 213 average time/residue: 0.8248 time to fit residues: 192.8462 Evaluate side-chains 160 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 274 GLN B 76 GLN B 274 GLN C 76 GLN C 274 GLN D 76 GLN D 274 GLN E 76 GLN E 274 GLN F 76 GLN F 274 GLN G 76 GLN G 274 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.083012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063479 restraints weight = 46842.036| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.40 r_work: 0.2880 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20167 Z= 0.163 Angle : 0.645 13.339 27377 Z= 0.305 Chirality : 0.041 0.149 3255 Planarity : 0.004 0.039 3178 Dihedral : 15.215 120.559 4522 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.44 % Allowed : 11.84 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 2380 helix: 1.32 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.42 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 29 TYR 0.014 0.001 TYR A 10 PHE 0.010 0.001 PHE F 54 TRP 0.010 0.001 TRP A 104 HIS 0.003 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00378 (20146) covalent geometry : angle 0.64333 (27328) SS BOND : bond 0.00363 ( 14) SS BOND : angle 0.73487 ( 28) hydrogen bonds : bond 0.04027 ( 1226) hydrogen bonds : angle 4.07877 ( 3531) link_NAG-ASN : bond 0.00458 ( 7) link_NAG-ASN : angle 1.49497 ( 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 213 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.735 Fit side-chains REVERT: A 9 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 337 GLU cc_start: 0.8691 (tp30) cc_final: 0.8461 (tm-30) REVERT: B 5 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: B 9 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8152 (tm-30) REVERT: B 138 ASP cc_start: 0.8857 (m-30) cc_final: 0.8644 (m-30) REVERT: B 337 GLU cc_start: 0.8781 (tp30) cc_final: 0.8368 (tm-30) REVERT: B 352 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8923 (tp30) REVERT: C 5 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 9 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8166 (tm-30) REVERT: C 29 ARG cc_start: 0.8661 (mmt90) cc_final: 0.8173 (mmm-85) REVERT: C 254 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8613 (tpp80) REVERT: C 337 GLU cc_start: 0.8850 (tp30) cc_final: 0.8629 (tp30) REVERT: D 5 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: D 29 ARG cc_start: 0.8574 (mpt-90) cc_final: 0.8297 (mmt90) REVERT: D 337 GLU cc_start: 0.8729 (tp30) cc_final: 0.8394 (tm-30) REVERT: E 5 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8309 (tm-30) REVERT: E 9 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8215 (tm-30) REVERT: E 337 GLU cc_start: 0.8752 (tp30) cc_final: 0.8352 (tm-30) REVERT: F 5 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8183 (tm-30) REVERT: F 9 GLU cc_start: 0.8643 (tt0) cc_final: 0.8276 (tm-30) REVERT: F 337 GLU cc_start: 0.8704 (tp30) cc_final: 0.8303 (tm-30) REVERT: G 5 GLN cc_start: 0.8858 (mt0) cc_final: 0.8593 (tm-30) REVERT: G 9 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8112 (tm-30) REVERT: G 29 ARG cc_start: 0.8543 (mpt-90) cc_final: 0.8322 (mmt90) REVERT: G 337 GLU cc_start: 0.8699 (tp30) cc_final: 0.8468 (tm-30) outliers start: 45 outliers final: 11 residues processed: 200 average time/residue: 0.6431 time to fit residues: 144.3865 Evaluate side-chains 166 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 135 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 70 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 219 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 134 HIS B 134 HIS C 89 GLN C 134 HIS D 134 HIS E 89 GLN E 134 HIS F 134 HIS G 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.083345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.063619 restraints weight = 47512.807| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.45 r_work: 0.2894 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1837 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= 0.145 Angle : 0.603 12.619 27377 Z= 0.285 Chirality : 0.040 0.138 3255 Planarity : 0.004 0.038 3178 Dihedral : 13.032 91.977 4522 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.96 % Allowed : 14.18 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2380 helix: 1.69 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.19 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 29 TYR 0.010 0.001 TYR C 10 PHE 0.010 0.001 PHE F 54 TRP 0.010 0.001 TRP E 104 HIS 0.003 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00339 (20146) covalent geometry : angle 0.60238 (27328) SS BOND : bond 0.00345 ( 14) SS BOND : angle 0.63065 ( 28) hydrogen bonds : bond 0.03701 ( 1226) hydrogen bonds : angle 3.86862 ( 3531) link_NAG-ASN : bond 0.00471 ( 7) link_NAG-ASN : angle 1.35387 ( 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 200 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.735 Fit side-chains REVERT: A 9 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: A 337 GLU cc_start: 0.8653 (tp30) cc_final: 0.8388 (tm-30) REVERT: B 5 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8536 (tm-30) REVERT: B 9 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 254 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8605 (tpp80) REVERT: B 337 GLU cc_start: 0.8829 (tp30) cc_final: 0.8535 (tm-30) REVERT: B 352 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8915 (tp30) REVERT: C 5 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8317 (tm-30) REVERT: C 9 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 29 ARG cc_start: 0.8587 (mmt90) cc_final: 0.8127 (mmm-85) REVERT: C 89 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8687 (mm-40) REVERT: C 254 ARG cc_start: 0.8844 (tpp80) cc_final: 0.8629 (tpp80) REVERT: C 337 GLU cc_start: 0.8818 (tp30) cc_final: 0.8551 (tp30) REVERT: D 5 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: D 9 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8105 (tm-30) REVERT: D 29 ARG cc_start: 0.8472 (mpt-90) cc_final: 0.8254 (mmt90) REVERT: D 56 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8654 (pp30) REVERT: D 337 GLU cc_start: 0.8686 (tp30) cc_final: 0.8402 (tm-30) REVERT: E 5 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8234 (tm-30) REVERT: E 9 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8205 (tm-30) REVERT: E 337 GLU cc_start: 0.8702 (tp30) cc_final: 0.8477 (tm-30) REVERT: F 5 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 9 GLU cc_start: 0.8756 (tt0) cc_final: 0.8443 (tm-30) REVERT: F 29 ARG cc_start: 0.8534 (mmt90) cc_final: 0.8091 (mmt90) REVERT: F 254 ARG cc_start: 0.8884 (tpp80) cc_final: 0.8677 (tpp80) REVERT: F 337 GLU cc_start: 0.8740 (tp30) cc_final: 0.8255 (tm-30) REVERT: G 5 GLN cc_start: 0.8822 (mt0) cc_final: 0.8594 (tm-30) REVERT: G 9 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8073 (tm-30) REVERT: G 337 GLU cc_start: 0.8677 (tp30) cc_final: 0.8460 (tm-30) outliers start: 36 outliers final: 11 residues processed: 188 average time/residue: 0.6982 time to fit residues: 146.0709 Evaluate side-chains 171 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 258 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN E 89 GLN G 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064605 restraints weight = 47249.229| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.48 r_work: 0.2921 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20167 Z= 0.122 Angle : 0.571 12.564 27377 Z= 0.271 Chirality : 0.038 0.134 3255 Planarity : 0.004 0.038 3178 Dihedral : 12.385 86.389 4522 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.37 % Allowed : 13.80 % Favored : 82.84 % 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: 1.01 (0.18), residues: 2380 helix: 1.89 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.22 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 29 TYR 0.009 0.001 TYR C 10 PHE 0.009 0.001 PHE C 54 TRP 0.014 0.001 TRP C 104 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00280 (20146) covalent geometry : angle 0.57033 (27328) SS BOND : bond 0.00276 ( 14) SS BOND : angle 0.53756 ( 28) hydrogen bonds : bond 0.03406 ( 1226) hydrogen bonds : angle 3.72583 ( 3531) link_NAG-ASN : bond 0.00522 ( 7) link_NAG-ASN : angle 1.34339 ( 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 229 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 0.478 Fit side-chains REVERT: A 9 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: A 56 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8582 (pp30) REVERT: A 254 ARG cc_start: 0.8871 (tpp80) cc_final: 0.8569 (tpp80) REVERT: A 337 GLU cc_start: 0.8629 (tp30) cc_final: 0.8273 (tm-30) REVERT: B 5 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: B 9 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: B 254 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8652 (tpp80) REVERT: B 337 GLU cc_start: 0.8839 (tp30) cc_final: 0.8600 (tm-30) REVERT: B 352 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8916 (tp30) REVERT: C 5 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8403 (tm-30) REVERT: C 9 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: C 29 ARG cc_start: 0.8560 (mmt90) cc_final: 0.8123 (mmm-85) REVERT: C 254 ARG cc_start: 0.8863 (tpp80) cc_final: 0.8653 (tpp80) REVERT: C 337 GLU cc_start: 0.8824 (tp30) cc_final: 0.8580 (tp30) REVERT: D 5 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: D 9 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8203 (tm-30) REVERT: D 29 ARG cc_start: 0.8402 (mpt-90) cc_final: 0.8198 (mmt90) REVERT: D 56 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8578 (pp30) REVERT: D 254 ARG cc_start: 0.8666 (tpp80) cc_final: 0.8349 (tpp80) REVERT: D 337 GLU cc_start: 0.8660 (tp30) cc_final: 0.8408 (tm-30) REVERT: E 5 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8308 (tm-30) REVERT: E 9 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: E 56 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8626 (pp30) REVERT: E 57 GLU cc_start: 0.8388 (pm20) cc_final: 0.8165 (pm20) REVERT: E 337 GLU cc_start: 0.8719 (tp30) cc_final: 0.8139 (tm-30) REVERT: F 5 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8368 (tm-30) REVERT: F 9 GLU cc_start: 0.8800 (tt0) cc_final: 0.8437 (tm-30) REVERT: F 29 ARG cc_start: 0.8442 (mmt90) cc_final: 0.8009 (mmt90) REVERT: F 337 GLU cc_start: 0.8760 (tp30) cc_final: 0.8263 (tm-30) REVERT: G 5 GLN cc_start: 0.8858 (mt0) cc_final: 0.8606 (tm-30) REVERT: G 9 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: G 337 GLU cc_start: 0.8692 (tp30) cc_final: 0.8460 (tm-30) outliers start: 62 outliers final: 21 residues processed: 209 average time/residue: 0.6733 time to fit residues: 157.0112 Evaluate side-chains 185 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 93 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 89 GLN E 89 GLN F 89 GLN G 134 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.081005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.060698 restraints weight = 47618.979| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.44 r_work: 0.2824 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 20167 Z= 0.255 Angle : 0.663 12.345 27377 Z= 0.314 Chirality : 0.041 0.139 3255 Planarity : 0.004 0.039 3178 Dihedral : 12.570 88.403 4522 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.99 % Allowed : 15.26 % Favored : 81.75 % 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: 0.91 (0.18), residues: 2380 helix: 1.80 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.22 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 254 TYR 0.013 0.002 TYR A 10 PHE 0.016 0.002 PHE F 54 TRP 0.008 0.001 TRP E 104 HIS 0.001 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00606 (20146) covalent geometry : angle 0.66236 (27328) SS BOND : bond 0.00604 ( 14) SS BOND : angle 1.07906 ( 28) hydrogen bonds : bond 0.03907 ( 1226) hydrogen bonds : angle 3.93584 ( 3531) link_NAG-ASN : bond 0.00350 ( 7) link_NAG-ASN : angle 1.16965 ( 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 214 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.574 Fit side-chains REVERT: A 9 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: A 254 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8661 (tpp80) REVERT: A 337 GLU cc_start: 0.8592 (tp30) cc_final: 0.8031 (tm-30) REVERT: B 5 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8576 (tm-30) REVERT: B 9 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: B 31 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8387 (tt0) REVERT: B 254 ARG cc_start: 0.8877 (tpp80) cc_final: 0.8653 (tpp80) REVERT: B 337 GLU cc_start: 0.8803 (tp30) cc_final: 0.8335 (tm-30) REVERT: B 352 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8928 (tp30) REVERT: C 5 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 9 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: C 29 ARG cc_start: 0.8681 (mmt90) cc_final: 0.8187 (mmm-85) REVERT: C 337 GLU cc_start: 0.8803 (tp30) cc_final: 0.8583 (tp30) REVERT: D 5 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8598 (tm-30) REVERT: D 9 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8109 (tm-30) REVERT: D 29 ARG cc_start: 0.8581 (mpt-90) cc_final: 0.8241 (mmt90) REVERT: E 5 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8367 (tm-30) REVERT: E 9 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: E 337 GLU cc_start: 0.8679 (tp30) cc_final: 0.8000 (tm-30) REVERT: E 352 GLU cc_start: 0.9207 (tp30) cc_final: 0.8939 (tm-30) REVERT: F 5 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8493 (tm-30) REVERT: F 9 GLU cc_start: 0.8776 (tt0) cc_final: 0.8514 (tm-30) REVERT: F 29 ARG cc_start: 0.8658 (mmt90) cc_final: 0.8066 (mmm-85) REVERT: F 337 GLU cc_start: 0.8744 (tp30) cc_final: 0.8317 (tm-30) REVERT: G 5 GLN cc_start: 0.8860 (mt0) cc_final: 0.8606 (tm-30) REVERT: G 9 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: G 29 ARG cc_start: 0.8674 (mmt90) cc_final: 0.8224 (mmt90) REVERT: G 254 ARG cc_start: 0.8756 (tpp80) cc_final: 0.8491 (tpp80) REVERT: G 337 GLU cc_start: 0.8699 (tp30) cc_final: 0.8231 (tm-30) outliers start: 55 outliers final: 31 residues processed: 202 average time/residue: 0.6604 time to fit residues: 148.8918 Evaluate side-chains 188 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 5 GLN Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 6 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 209 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.083719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.064295 restraints weight = 46911.945| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.46 r_work: 0.2912 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2366 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= 0.120 Angle : 0.563 9.940 27377 Z= 0.272 Chirality : 0.038 0.140 3255 Planarity : 0.004 0.039 3178 Dihedral : 11.971 78.749 4522 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.61 % Allowed : 16.68 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2380 helix: 1.94 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.12 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 254 TYR 0.009 0.001 TYR B 230 PHE 0.012 0.001 PHE D 54 TRP 0.009 0.001 TRP A 104 HIS 0.003 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00276 (20146) covalent geometry : angle 0.56177 (27328) SS BOND : bond 0.00291 ( 14) SS BOND : angle 0.66053 ( 28) hydrogen bonds : bond 0.03348 ( 1226) hydrogen bonds : angle 3.74168 ( 3531) link_NAG-ASN : bond 0.00416 ( 7) link_NAG-ASN : angle 1.15683 ( 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 209 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.743 Fit side-chains REVERT: A 9 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: A 56 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8575 (pp30) REVERT: A 242 ASP cc_start: 0.9094 (p0) cc_final: 0.8846 (p0) REVERT: A 254 ARG cc_start: 0.8906 (tpp80) cc_final: 0.8608 (tpp80) REVERT: A 337 GLU cc_start: 0.8606 (tp30) cc_final: 0.8243 (tm-30) REVERT: A 352 GLU cc_start: 0.9115 (tp30) cc_final: 0.8750 (tm-30) REVERT: B 9 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: B 31 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8397 (tt0) REVERT: B 254 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8608 (tpp80) REVERT: B 337 GLU cc_start: 0.8773 (tp30) cc_final: 0.8554 (tm-30) REVERT: B 352 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8856 (tm-30) REVERT: C 5 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8491 (tm-30) REVERT: C 9 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: C 29 ARG cc_start: 0.8566 (mmt90) cc_final: 0.8100 (mmm-85) REVERT: C 261 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8918 (t0) REVERT: C 337 GLU cc_start: 0.8823 (tp30) cc_final: 0.8595 (tp30) REVERT: D 9 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8297 (tm-30) REVERT: D 29 ARG cc_start: 0.8410 (mpt-90) cc_final: 0.8098 (mmt90) REVERT: D 56 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8547 (tm-30) REVERT: D 254 ARG cc_start: 0.8609 (tpp80) cc_final: 0.8306 (tpp80) REVERT: D 261 ASP cc_start: 0.9220 (m-30) cc_final: 0.9008 (t0) REVERT: E 5 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8391 (tm-30) REVERT: E 9 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: E 254 ARG cc_start: 0.8960 (tpp80) cc_final: 0.8749 (tpp80) REVERT: E 337 GLU cc_start: 0.8681 (tp30) cc_final: 0.8117 (tm-30) REVERT: F 5 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8465 (tm-30) REVERT: F 9 GLU cc_start: 0.8774 (tt0) cc_final: 0.8538 (tm-30) REVERT: F 31 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8468 (tt0) REVERT: G 5 GLN cc_start: 0.8791 (mt0) cc_final: 0.8574 (tm-30) REVERT: G 9 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: G 254 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8431 (tpp80) REVERT: G 261 ASP cc_start: 0.9036 (OUTLIER) cc_final: 0.8786 (t0) REVERT: G 337 GLU cc_start: 0.8645 (tp30) cc_final: 0.8366 (tm-30) outliers start: 48 outliers final: 24 residues processed: 192 average time/residue: 0.6915 time to fit residues: 148.0598 Evaluate side-chains 186 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.083632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.064090 restraints weight = 47187.491| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.47 r_work: 0.2910 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2466 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= 0.128 Angle : 0.568 7.813 27377 Z= 0.274 Chirality : 0.038 0.135 3255 Planarity : 0.004 0.038 3178 Dihedral : 11.716 73.627 4522 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.44 % Allowed : 16.84 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.19), residues: 2380 helix: 2.01 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.05 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 254 TYR 0.009 0.001 TYR B 345 PHE 0.010 0.001 PHE F 54 TRP 0.009 0.001 TRP E 104 HIS 0.001 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00300 (20146) covalent geometry : angle 0.56683 (27328) SS BOND : bond 0.00292 ( 14) SS BOND : angle 0.64463 ( 28) hydrogen bonds : bond 0.03286 ( 1226) hydrogen bonds : angle 3.69105 ( 3531) link_NAG-ASN : bond 0.00398 ( 7) link_NAG-ASN : angle 1.13634 ( 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 200 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.686 Fit side-chains REVERT: A 9 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: A 56 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8529 (pp30) REVERT: A 254 ARG cc_start: 0.8929 (tpp80) cc_final: 0.8630 (tpp80) REVERT: A 337 GLU cc_start: 0.8587 (tp30) cc_final: 0.8149 (tm-30) REVERT: B 9 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: B 31 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8366 (tt0) REVERT: B 254 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8621 (tpp80) REVERT: B 337 GLU cc_start: 0.8770 (tp30) cc_final: 0.8553 (tm-30) REVERT: B 352 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8853 (tm-30) REVERT: C 5 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8490 (tm-30) REVERT: C 9 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: C 29 ARG cc_start: 0.8556 (mmt90) cc_final: 0.8076 (mmm-85) REVERT: C 337 GLU cc_start: 0.8831 (tp30) cc_final: 0.8569 (tp30) REVERT: D 9 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8136 (tm-30) REVERT: D 29 ARG cc_start: 0.8339 (mpt-90) cc_final: 0.8117 (mmt90) REVERT: D 56 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8569 (tm-30) REVERT: D 254 ARG cc_start: 0.8666 (tpp80) cc_final: 0.8346 (tpp80) REVERT: D 352 GLU cc_start: 0.9082 (tp30) cc_final: 0.8656 (tm-30) REVERT: E 5 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8429 (tm-30) REVERT: E 9 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8168 (tm-30) REVERT: E 254 ARG cc_start: 0.8978 (tpp80) cc_final: 0.8732 (tpp80) REVERT: E 337 GLU cc_start: 0.8686 (tp30) cc_final: 0.8097 (tm-30) REVERT: E 352 GLU cc_start: 0.9150 (tp30) cc_final: 0.8823 (tm-30) REVERT: F 5 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8480 (tm-30) REVERT: F 9 GLU cc_start: 0.8793 (tt0) cc_final: 0.8539 (tm-30) REVERT: F 31 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8428 (tt0) REVERT: F 337 GLU cc_start: 0.8738 (tp30) cc_final: 0.8122 (tm-30) REVERT: G 5 GLN cc_start: 0.8793 (mt0) cc_final: 0.8587 (tm-30) REVERT: G 9 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: G 254 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8459 (tpp80) REVERT: G 261 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8818 (t0) REVERT: G 337 GLU cc_start: 0.8653 (tp30) cc_final: 0.8394 (tm-30) outliers start: 45 outliers final: 20 residues processed: 189 average time/residue: 0.6688 time to fit residues: 141.1817 Evaluate side-chains 176 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 308 VAL 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: 3.9990 chunk 193 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 210 optimal weight: 0.0770 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN C 89 GLN C 264 GLN D 208 ASN E 89 GLN E 208 ASN F 208 ASN G 208 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.085118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.065931 restraints weight = 47247.946| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.49 r_work: 0.2958 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20167 Z= 0.110 Angle : 0.546 7.621 27377 Z= 0.265 Chirality : 0.038 0.135 3255 Planarity : 0.004 0.039 3178 Dihedral : 11.283 76.461 4522 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.17 % Allowed : 17.49 % Favored : 80.34 % 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: 1.40 (0.19), residues: 2380 helix: 2.15 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -1.99 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 254 TYR 0.010 0.001 TYR C 345 PHE 0.010 0.001 PHE D 54 TRP 0.009 0.001 TRP C 104 HIS 0.003 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00249 (20146) covalent geometry : angle 0.54562 (27328) SS BOND : bond 0.00208 ( 14) SS BOND : angle 0.48866 ( 28) hydrogen bonds : bond 0.03042 ( 1226) hydrogen bonds : angle 3.60232 ( 3531) link_NAG-ASN : bond 0.00398 ( 7) link_NAG-ASN : angle 1.14156 ( 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 202 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.749 Fit side-chains REVERT: A 9 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: A 56 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8589 (pp30) REVERT: A 57 GLU cc_start: 0.8566 (pm20) cc_final: 0.8225 (pm20) REVERT: A 254 ARG cc_start: 0.8950 (tpp80) cc_final: 0.8712 (tpp80) REVERT: A 337 GLU cc_start: 0.8587 (tp30) cc_final: 0.8289 (tm-30) REVERT: A 352 GLU cc_start: 0.9083 (tp30) cc_final: 0.8785 (tm-30) REVERT: B 9 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: B 31 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8325 (tt0) REVERT: B 254 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8620 (tpp80) REVERT: B 337 GLU cc_start: 0.8774 (tp30) cc_final: 0.8529 (tm-30) REVERT: B 352 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8847 (tm-30) REVERT: C 5 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 9 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 29 ARG cc_start: 0.8442 (mmt90) cc_final: 0.7877 (mmm-85) REVERT: C 56 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8418 (pp30) REVERT: C 89 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8641 (mm-40) REVERT: C 337 GLU cc_start: 0.8836 (tp30) cc_final: 0.8227 (tm-30) REVERT: C 352 GLU cc_start: 0.9150 (tp30) cc_final: 0.8874 (tm-30) REVERT: D 9 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8147 (tm-30) REVERT: D 29 ARG cc_start: 0.8236 (mpt-90) cc_final: 0.7893 (mmt90) REVERT: D 56 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8521 (pp30) REVERT: D 254 ARG cc_start: 0.8669 (tpp80) cc_final: 0.8380 (tpp80) REVERT: D 337 GLU cc_start: 0.8673 (tp30) cc_final: 0.8110 (tm-30) REVERT: D 352 GLU cc_start: 0.9117 (tp30) cc_final: 0.8716 (tm-30) REVERT: E 5 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8433 (tm-30) REVERT: E 9 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8230 (tm-30) REVERT: E 56 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8452 (pp30) REVERT: E 57 GLU cc_start: 0.8541 (pm20) cc_final: 0.8147 (pm20) REVERT: E 254 ARG cc_start: 0.8952 (tpp80) cc_final: 0.8726 (tpp80) REVERT: E 337 GLU cc_start: 0.8660 (tp30) cc_final: 0.8120 (tm-30) REVERT: E 352 GLU cc_start: 0.9153 (tp30) cc_final: 0.8900 (tm-30) REVERT: F 5 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8484 (tm-30) REVERT: F 9 GLU cc_start: 0.8838 (tt0) cc_final: 0.8541 (tm-30) REVERT: F 29 ARG cc_start: 0.8306 (mmt90) cc_final: 0.7796 (mmm-85) REVERT: F 31 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8362 (tt0) REVERT: F 337 GLU cc_start: 0.8774 (tp30) cc_final: 0.8083 (tm-30) REVERT: G 9 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: G 56 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8622 (pp30) REVERT: G 254 ARG cc_start: 0.8714 (tpp80) cc_final: 0.8479 (tpp80) REVERT: G 337 GLU cc_start: 0.8642 (tp30) cc_final: 0.8403 (tm-30) outliers start: 40 outliers final: 20 residues processed: 191 average time/residue: 0.6642 time to fit residues: 142.1820 Evaluate side-chains 182 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 225 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.0000 chunk 165 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.082465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.062802 restraints weight = 47095.106| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.46 r_work: 0.2880 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20167 Z= 0.178 Angle : 0.601 8.392 27377 Z= 0.291 Chirality : 0.039 0.133 3255 Planarity : 0.004 0.037 3178 Dihedral : 11.502 77.811 4522 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.63 % Allowed : 18.25 % Favored : 80.12 % 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 (0.19), residues: 2380 helix: 2.29 (0.14), residues: 1589 sheet: None (None), residues: 0 loop : -1.54 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 254 TYR 0.010 0.001 TYR C 10 PHE 0.012 0.001 PHE D 54 TRP 0.006 0.001 TRP D 74 HIS 0.001 0.000 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00426 (20146) covalent geometry : angle 0.60034 (27328) SS BOND : bond 0.00424 ( 14) SS BOND : angle 0.86814 ( 28) hydrogen bonds : bond 0.03473 ( 1226) hydrogen bonds : angle 3.72634 ( 3531) link_NAG-ASN : bond 0.00311 ( 7) link_NAG-ASN : angle 0.96156 ( 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 182 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.718 Fit side-chains REVERT: A 9 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: A 254 ARG cc_start: 0.8948 (tpp80) cc_final: 0.8655 (tpp80) REVERT: A 337 GLU cc_start: 0.8601 (tp30) cc_final: 0.8220 (tm-30) REVERT: A 352 GLU cc_start: 0.9139 (tp30) cc_final: 0.8828 (tm-30) REVERT: B 9 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: B 31 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8322 (tt0) REVERT: B 254 ARG cc_start: 0.8879 (tpp80) cc_final: 0.8638 (tpp80) REVERT: B 337 GLU cc_start: 0.8810 (tp30) cc_final: 0.8490 (tm-30) REVERT: B 352 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8882 (tm-30) REVERT: C 5 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 9 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: C 29 ARG cc_start: 0.8589 (mmt90) cc_final: 0.8121 (mmm-85) REVERT: C 337 GLU cc_start: 0.8865 (tp30) cc_final: 0.8618 (tp30) REVERT: D 9 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8172 (tm-30) REVERT: D 29 ARG cc_start: 0.8394 (mpt-90) cc_final: 0.7904 (mmt90) REVERT: D 337 GLU cc_start: 0.8713 (tp30) cc_final: 0.7952 (tm-30) REVERT: E 5 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 9 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8199 (tm-30) REVERT: E 337 GLU cc_start: 0.8690 (tp30) cc_final: 0.8140 (tm-30) REVERT: E 352 GLU cc_start: 0.9189 (tp30) cc_final: 0.8920 (tm-30) REVERT: F 5 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8539 (tm-30) REVERT: F 9 GLU cc_start: 0.8837 (tt0) cc_final: 0.8440 (tm-30) REVERT: F 29 ARG cc_start: 0.8464 (mmt90) cc_final: 0.7788 (mmm-85) REVERT: F 31 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8442 (tt0) REVERT: F 337 GLU cc_start: 0.8730 (tp30) cc_final: 0.8041 (tm-30) REVERT: F 352 GLU cc_start: 0.9158 (tp30) cc_final: 0.8900 (tm-30) REVERT: G 9 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: G 56 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8601 (pp30) REVERT: G 254 ARG cc_start: 0.8720 (tpp80) cc_final: 0.8480 (tpp80) REVERT: G 337 GLU cc_start: 0.8697 (tp30) cc_final: 0.8453 (tm-30) outliers start: 30 outliers final: 18 residues processed: 177 average time/residue: 0.6968 time to fit residues: 137.3531 Evaluate side-chains 172 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 43 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 137 optimal weight: 0.0010 chunk 124 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.083556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.064064 restraints weight = 47078.410| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.47 r_work: 0.2909 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20167 Z= 0.134 Angle : 0.571 7.666 27377 Z= 0.278 Chirality : 0.038 0.135 3255 Planarity : 0.004 0.038 3178 Dihedral : 11.375 80.271 4522 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.36 % Allowed : 18.63 % Favored : 80.01 % 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: 1.38 (0.19), residues: 2380 helix: 2.11 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 254 TYR 0.009 0.001 TYR C 10 PHE 0.012 0.001 PHE D 54 TRP 0.007 0.001 TRP C 104 HIS 0.001 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00318 (20146) covalent geometry : angle 0.57030 (27328) SS BOND : bond 0.00313 ( 14) SS BOND : angle 0.72960 ( 28) hydrogen bonds : bond 0.03262 ( 1226) hydrogen bonds : angle 3.67681 ( 3531) link_NAG-ASN : bond 0.00342 ( 7) link_NAG-ASN : angle 0.96558 ( 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 183 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.720 Fit side-chains REVERT: A 9 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: A 56 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8623 (pp30) REVERT: A 242 ASP cc_start: 0.9059 (p0) cc_final: 0.8829 (p0) REVERT: A 254 ARG cc_start: 0.8950 (tpp80) cc_final: 0.8686 (tpp80) REVERT: A 337 GLU cc_start: 0.8587 (tp30) cc_final: 0.8270 (tm-30) REVERT: A 352 GLU cc_start: 0.9105 (tp30) cc_final: 0.8822 (tm-30) REVERT: B 9 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: B 31 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8342 (tt0) REVERT: B 254 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8617 (tpp80) REVERT: B 352 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8864 (tm-30) REVERT: C 5 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8510 (tm-30) REVERT: C 9 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 29 ARG cc_start: 0.8547 (mmt90) cc_final: 0.7840 (mmm-85) REVERT: C 337 GLU cc_start: 0.8813 (tp30) cc_final: 0.8212 (tm-30) REVERT: C 352 GLU cc_start: 0.9144 (tp30) cc_final: 0.8901 (tm-30) REVERT: D 9 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8187 (tm-30) REVERT: D 29 ARG cc_start: 0.8383 (mpt-90) cc_final: 0.7976 (mmt90) REVERT: D 56 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8541 (pp30) REVERT: D 254 ARG cc_start: 0.8740 (tpp80) cc_final: 0.8448 (tpp80) REVERT: D 337 GLU cc_start: 0.8717 (tp30) cc_final: 0.8118 (tm-30) REVERT: D 352 GLU cc_start: 0.9073 (tp30) cc_final: 0.8700 (tm-30) REVERT: E 5 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8460 (tm-30) REVERT: E 9 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8203 (tm-30) REVERT: E 337 GLU cc_start: 0.8662 (tp30) cc_final: 0.8128 (tm-30) REVERT: E 352 GLU cc_start: 0.9192 (tp30) cc_final: 0.8935 (tm-30) REVERT: F 5 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8516 (tm-30) REVERT: F 9 GLU cc_start: 0.8840 (tt0) cc_final: 0.8537 (tm-30) REVERT: F 29 ARG cc_start: 0.8363 (mmt90) cc_final: 0.7786 (mmm-85) REVERT: F 31 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8466 (tt0) REVERT: F 337 GLU cc_start: 0.8742 (tp30) cc_final: 0.8096 (tm-30) REVERT: F 352 GLU cc_start: 0.9144 (tp30) cc_final: 0.8886 (tm-30) REVERT: G 9 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: G 56 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8553 (pp30) REVERT: G 254 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8459 (tpp80) REVERT: G 337 GLU cc_start: 0.8670 (tp30) cc_final: 0.7951 (tm-30) REVERT: G 352 GLU cc_start: 0.9120 (tp30) cc_final: 0.8889 (tm-30) outliers start: 25 outliers final: 17 residues processed: 176 average time/residue: 0.6827 time to fit residues: 134.2194 Evaluate side-chains 176 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 9 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 73 optimal weight: 0.2980 chunk 164 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 108 optimal weight: 0.0980 chunk 159 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN E 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.084022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064437 restraints weight = 47228.728| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.50 r_work: 0.2923 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20167 Z= 0.125 Angle : 0.568 7.647 27377 Z= 0.277 Chirality : 0.038 0.136 3255 Planarity : 0.004 0.038 3178 Dihedral : 11.243 84.377 4522 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.41 % Allowed : 18.79 % Favored : 79.79 % 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: 1.44 (0.19), residues: 2380 helix: 2.15 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 254 TYR 0.009 0.001 TYR C 10 PHE 0.012 0.001 PHE D 54 TRP 0.008 0.001 TRP C 104 HIS 0.001 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00294 (20146) covalent geometry : angle 0.56739 (27328) SS BOND : bond 0.00269 ( 14) SS BOND : angle 0.62266 ( 28) hydrogen bonds : bond 0.03192 ( 1226) hydrogen bonds : angle 3.64890 ( 3531) link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 0.95378 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4541.63 seconds wall clock time: 78 minutes 36.60 seconds (4716.60 seconds total)