Starting phenix.real_space_refine on Sun Sep 13 03:51:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wbg_21589/09_2026/6wbg_21589.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wbg_21589/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wbg_21589/09_2026/6wbg_21589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wbg_21589/09_2026/6wbg_21589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wbg_21589/09_2026/6wbg_21589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wbg_21589/09_2026/6wbg_21589.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wbg_21589/09_2026/6wbg_21589.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wbg_21589/09_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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19712 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "F" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2598 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 218 Unusual residues: {'3PE': 1, 'CLR': 2, 'DGA': 1, 'NAG': 1, 'PTY': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.87, per 1000 atoms: 0.20 Number of scatterers: 19712 At special positions: 0 Unit cell: (107.73, 108.756, 121.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 21 15.00 O 3381 8.00 N 2912 7.00 C 13321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 407 " - " ASN A 255 " " NAG B 407 " - " ASN B 255 " " NAG C 407 " - " ASN C 255 " " NAG D 407 " - " ASN D 255 " " NAG E 407 " - " ASN E 255 " " NAG F 407 " - " ASN F 255 " " NAG G 407 " - " ASN G 255 " Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 706.4 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: 0.47 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: 3.01 Time building geometry restraints manager: 2.21 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: 11285 29.68 - 59.37: 547 59.37 - 89.05: 32 89.05 - 118.73: 1 118.73 - 148.41: 14 Dihedral angle restraints: 11879 sinusoidal: 4704 harmonic: 7175 Sorted by residual: dihedral pdb=" N1 PTY A 401 " pdb=" C2 PTY A 401 " pdb=" C3 PTY A 401 " pdb=" O11 PTY A 401 " ideal model delta sinusoidal sigma weight residual 65.33 -83.08 148.41 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 11876 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.150 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 17.098 148.414 7175 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/Z covalent geometry : bond 0.00699 / 0.34 (20146) covalent geometry : angle 0.82747 / 0.46 (27328) SS BOND : bond 0.00249 / 0.16 ( 14) SS BOND : angle 0.73140 / 0.52 ( 28) hydrogen bonds : bond 0.14035 / 8.95 ( 1226) hydrogen bonds : angle 5.43804 / 3.87 ( 3531) link_NAG-ASN : bond 0.00607 / 0.40 ( 7) link_NAG-ASN : angle 0.88914 / 0.64 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.854 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: 0.8120 time to fit residues: 191.1416 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 : 0.616 ------------------------------------------------------------------------------- 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... 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 = 0.3505 r_free = 0.3505 target = 0.083007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063213 restraints weight = 46893.293| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.43 r_work: 0.2881 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1550 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= 0.162 Angle : 0.644 13.770 27377 Z= 0.304 Chirality : 0.040 0.139 3255 Planarity : 0.004 0.039 3178 Dihedral : 15.313 117.674 3353 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.39 % Allowed : 11.90 % 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: 0.31 (0.18), residues: 2380 helix: 1.34 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -2.41 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 29 TYR 0.015 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/Z covalent geometry : bond 0.00377 / 0.16 (20146) covalent geometry : angle 0.64251 / 0.30 (27328) SS BOND : bond 0.00371 / 0.24 ( 14) SS BOND : angle 0.72450 / 0.51 ( 28) hydrogen bonds : bond 0.03956 / 2.60 ( 1226) hydrogen bonds : angle 4.06222 / 2.89 ( 3531) link_NAG-ASN : bond 0.00572 / 0.37 ( 7) link_NAG-ASN : angle 1.45285 / 1.02 ( 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 212 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.813 Fit side-chains REVERT: A 9 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8111 (tm-30) REVERT: A 337 GLU cc_start: 0.8689 (tp30) cc_final: 0.8464 (tm-30) REVERT: B 5 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: B 9 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 138 ASP cc_start: 0.8855 (m-30) cc_final: 0.8644 (m-30) REVERT: B 337 GLU cc_start: 0.8865 (tp30) cc_final: 0.8471 (tm-30) REVERT: B 352 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8921 (tp30) REVERT: C 5 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 9 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 29 ARG cc_start: 0.8655 (mmt90) cc_final: 0.8160 (mmm-85) REVERT: C 254 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8585 (tpp80) REVERT: C 337 GLU cc_start: 0.8845 (tp30) cc_final: 0.8625 (tp30) REVERT: D 5 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8606 (tm-30) REVERT: D 9 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8195 (tm-30) REVERT: D 29 ARG cc_start: 0.8540 (mpt-90) cc_final: 0.8268 (mmt90) REVERT: D 337 GLU cc_start: 0.8724 (tp30) cc_final: 0.8396 (tm-30) REVERT: E 5 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8256 (tm-30) REVERT: E 9 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8103 (tm-30) REVERT: E 337 GLU cc_start: 0.8750 (tp30) cc_final: 0.8110 (tm-30) REVERT: F 5 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8204 (tm-30) REVERT: F 9 GLU cc_start: 0.8654 (tt0) cc_final: 0.8288 (tm-30) REVERT: F 254 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8634 (tpp80) REVERT: F 337 GLU cc_start: 0.8706 (tp30) cc_final: 0.8300 (tm-30) REVERT: G 5 GLN cc_start: 0.8850 (mt0) cc_final: 0.8594 (tm-30) REVERT: G 9 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 29 ARG cc_start: 0.8532 (mpt-90) cc_final: 0.8326 (mmt90) REVERT: G 337 GLU cc_start: 0.8702 (tp30) cc_final: 0.8476 (tm-30) outliers start: 44 outliers final: 11 residues processed: 199 average time/residue: 0.6775 time to fit residues: 152.0301 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 : 0.771 ------------------------------------------------------------------------------- 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: 0.4980 chunk 50 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 103 optimal weight: 0.0470 chunk 135 optimal weight: 6.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN A 134 HIS C 89 GLN E 89 GLN E 134 HIS F 134 HIS G 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065579 restraints weight = 47258.962| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.51 r_work: 0.2941 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20167 Z= 0.113 Angle : 0.573 11.844 27377 Z= 0.273 Chirality : 0.039 0.134 3255 Planarity : 0.004 0.038 3178 Dihedral : 12.460 100.624 3353 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.01 % Allowed : 13.80 % Favored : 84.19 % 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: 1.78 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.17 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 29 TYR 0.009 0.001 TYR B 230 PHE 0.008 0.001 PHE C 54 TRP 0.009 0.001 TRP E 104 HIS 0.003 0.001 HIS F 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (20146) covalent geometry : angle 0.57243 / 0.27 (27328) SS BOND : bond 0.00232 / 0.15 ( 14) SS BOND : angle 0.42145 / 0.31 ( 28) hydrogen bonds : bond 0.03482 / 2.30 ( 1226) hydrogen bonds : angle 3.78680 / 2.69 ( 3531) link_NAG-ASN : bond 0.00464 / 0.29 ( 7) link_NAG-ASN : angle 1.35292 / 0.95 ( 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 203 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.779 Fit side-chains REVERT: A 9 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: A 29 ARG cc_start: 0.8496 (mmt90) cc_final: 0.8260 (mmt90) REVERT: A 56 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8512 (pp30) REVERT: A 254 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8525 (tpp80) REVERT: A 336 GLU cc_start: 0.8920 (tt0) cc_final: 0.8706 (tt0) REVERT: A 337 GLU cc_start: 0.8681 (tp30) cc_final: 0.8445 (tm-30) REVERT: B 5 GLN cc_start: 0.8762 (mt0) cc_final: 0.8512 (tm-30) REVERT: B 9 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 254 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8613 (tpp80) REVERT: B 337 GLU cc_start: 0.8873 (tp30) cc_final: 0.8589 (tm-30) REVERT: B 352 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8913 (tp30) REVERT: C 5 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8262 (tm-30) REVERT: C 9 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 29 ARG cc_start: 0.8565 (mmt90) cc_final: 0.8164 (mmt90) REVERT: C 89 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8750 (mm-40) REVERT: C 254 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8582 (tpp80) REVERT: C 337 GLU cc_start: 0.8832 (tp30) cc_final: 0.8490 (tp30) REVERT: D 5 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: D 9 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8178 (tm-30) REVERT: D 29 ARG cc_start: 0.8396 (mpt-90) cc_final: 0.8139 (mmt90) REVERT: D 56 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8548 (pp30) REVERT: D 337 GLU cc_start: 0.8694 (tp30) cc_final: 0.8487 (tp30) REVERT: E 5 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8229 (tm-30) REVERT: E 9 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8277 (tm-30) REVERT: E 29 ARG cc_start: 0.8465 (mmt90) cc_final: 0.8224 (mmt90) REVERT: E 56 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8534 (pp30) REVERT: E 337 GLU cc_start: 0.8746 (tp30) cc_final: 0.8409 (tm-30) REVERT: F 5 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8278 (tm-30) REVERT: F 9 GLU cc_start: 0.8788 (tt0) cc_final: 0.8400 (tm-30) REVERT: F 337 GLU cc_start: 0.8761 (tp30) cc_final: 0.8275 (tm-30) REVERT: G 5 GLN cc_start: 0.8770 (mt0) cc_final: 0.8527 (tm-30) REVERT: G 9 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8245 (tm-30) REVERT: G 337 GLU cc_start: 0.8656 (tp30) cc_final: 0.8451 (tm-30) outliers start: 37 outliers final: 8 residues processed: 193 average time/residue: 0.7222 time to fit residues: 155.6779 Evaluate side-chains 168 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 E residue 89 GLN Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 258 THR 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: 4.9990 chunk 120 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN C 89 GLN D 134 HIS E 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.084508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.064844 restraints weight = 47131.004| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.52 r_work: 0.2928 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20167 Z= 0.125 Angle : 0.563 12.188 27377 Z= 0.269 Chirality : 0.038 0.131 3255 Planarity : 0.004 0.037 3178 Dihedral : 11.682 97.483 3353 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.50 % Allowed : 14.18 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2380 helix: 1.92 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.21 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 254 TYR 0.009 0.001 TYR C 10 PHE 0.008 0.001 PHE C 54 TRP 0.012 0.001 TRP E 104 HIS 0.002 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (20146) covalent geometry : angle 0.56155 / 0.27 (27328) SS BOND : bond 0.00268 / 0.18 ( 14) SS BOND : angle 0.52912 / 0.38 ( 28) hydrogen bonds : bond 0.03361 / 2.23 ( 1226) hydrogen bonds : angle 3.68342 / 2.62 ( 3531) link_NAG-ASN : bond 0.00462 / 0.30 ( 7) link_NAG-ASN : angle 1.35373 / 0.93 ( 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 211 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.810 Fit side-chains REVERT: A 9 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: A 29 ARG cc_start: 0.8481 (mmt90) cc_final: 0.8169 (mmt90) REVERT: A 56 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8554 (pp30) REVERT: A 254 ARG cc_start: 0.8891 (tpp80) cc_final: 0.8577 (tpp80) REVERT: A 336 GLU cc_start: 0.8924 (tt0) cc_final: 0.8698 (tt0) REVERT: A 337 GLU cc_start: 0.8662 (tp30) cc_final: 0.8319 (tm-30) REVERT: B 5 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8525 (tm-30) REVERT: B 9 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: B 254 ARG cc_start: 0.8881 (tpp80) cc_final: 0.8656 (tpp80) REVERT: B 337 GLU cc_start: 0.8849 (tp30) cc_final: 0.8623 (tm-30) REVERT: B 352 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8927 (tp30) REVERT: C 5 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8369 (tm-30) REVERT: C 9 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8086 (tm-30) REVERT: C 29 ARG cc_start: 0.8559 (mmt90) cc_final: 0.8169 (mmm-85) REVERT: C 261 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8874 (t0) REVERT: C 337 GLU cc_start: 0.8862 (tp30) cc_final: 0.8606 (tp30) REVERT: D 5 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: D 9 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8158 (tm-30) REVERT: D 56 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8518 (pp30) REVERT: D 254 ARG cc_start: 0.8683 (tpp80) cc_final: 0.8359 (tpp80) REVERT: D 337 GLU cc_start: 0.8676 (tp30) cc_final: 0.8424 (tm-30) REVERT: E 5 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8271 (tm-30) REVERT: E 9 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8093 (tm-30) REVERT: E 56 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8580 (pp30) REVERT: E 337 GLU cc_start: 0.8733 (tp30) cc_final: 0.8154 (tm-30) REVERT: E 352 GLU cc_start: 0.9198 (tp30) cc_final: 0.8795 (tm-30) REVERT: F 5 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8349 (tm-30) REVERT: F 9 GLU cc_start: 0.8811 (tt0) cc_final: 0.8412 (tm-30) REVERT: F 56 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8507 (pp30) REVERT: F 337 GLU cc_start: 0.8763 (tp30) cc_final: 0.8286 (tm-30) REVERT: G 5 GLN cc_start: 0.8789 (mt0) cc_final: 0.8527 (tm-30) REVERT: G 9 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: G 261 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8745 (t0) REVERT: G 337 GLU cc_start: 0.8715 (tp30) cc_final: 0.8438 (tm-30) outliers start: 46 outliers final: 17 residues processed: 195 average time/residue: 0.7166 time to fit residues: 156.2665 Evaluate side-chains 181 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 258 THR Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR 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 5 GLN Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 9 GLU 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: 2.9990 chunk 112 optimal weight: 5.9990 chunk 183 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN C 89 GLN C 134 HIS G 134 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.082826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.063249 restraints weight = 47013.392| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.46 r_work: 0.2888 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20167 Z= 0.162 Angle : 0.583 10.434 27377 Z= 0.281 Chirality : 0.039 0.132 3255 Planarity : 0.004 0.043 3178 Dihedral : 11.329 94.285 3353 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.10 % Allowed : 15.05 % Favored : 81.86 % 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: 1.10 (0.18), residues: 2380 helix: 1.94 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.16 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 29 TYR 0.010 0.001 TYR C 10 PHE 0.012 0.001 PHE D 54 TRP 0.006 0.001 TRP B 74 HIS 0.001 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (20146) covalent geometry : angle 0.58161 / 0.28 (27328) SS BOND : bond 0.00392 / 0.26 ( 14) SS BOND : angle 0.78488 / 0.56 ( 28) hydrogen bonds : bond 0.03495 / 2.32 ( 1226) hydrogen bonds : angle 3.73069 / 2.66 ( 3531) link_NAG-ASN : bond 0.00399 / 0.26 ( 7) link_NAG-ASN : angle 1.22788 / 0.86 ( 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 218 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 0.779 Fit side-chains REVERT: A 9 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: A 254 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8612 (tpp80) REVERT: A 336 GLU cc_start: 0.8936 (tt0) cc_final: 0.8654 (tt0) REVERT: A 337 GLU cc_start: 0.8664 (tp30) cc_final: 0.8339 (tm-30) REVERT: B 9 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: B 254 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8675 (tpp80) REVERT: B 337 GLU cc_start: 0.8810 (tp30) cc_final: 0.8499 (tm-30) REVERT: B 352 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8863 (tm-30) REVERT: C 5 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8423 (tm-30) REVERT: C 9 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: C 29 ARG cc_start: 0.8592 (mmt90) cc_final: 0.8145 (mmm-85) REVERT: C 261 ASP cc_start: 0.9120 (m-30) cc_final: 0.8901 (t0) REVERT: C 337 GLU cc_start: 0.8830 (tp30) cc_final: 0.8543 (tp30) REVERT: D 9 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: D 56 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8555 (tm-30) REVERT: D 337 GLU cc_start: 0.8653 (tp30) cc_final: 0.7981 (tm-30) REVERT: E 5 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8348 (tm-30) REVERT: E 9 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: E 254 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8778 (tpp80) REVERT: E 337 GLU cc_start: 0.8704 (tp30) cc_final: 0.8129 (tm-30) REVERT: F 5 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8411 (tm-30) REVERT: F 9 GLU cc_start: 0.8771 (tt0) cc_final: 0.8548 (tm-30) REVERT: F 337 GLU cc_start: 0.8719 (tp30) cc_final: 0.8228 (tm-30) REVERT: G 5 GLN cc_start: 0.8807 (mt0) cc_final: 0.8561 (tm-30) REVERT: G 9 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: G 254 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8410 (tpp80) REVERT: G 261 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8791 (t0) REVERT: G 337 GLU cc_start: 0.8691 (tp30) cc_final: 0.8389 (tm-30) outliers start: 57 outliers final: 25 residues processed: 200 average time/residue: 0.6806 time to fit residues: 152.5342 Evaluate side-chains 187 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 9 GLU 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 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: 7.9990 chunk 191 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS C 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 = 0.084330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.065040 restraints weight = 46822.468| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.47 r_work: 0.2937 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20167 Z= 0.121 Angle : 0.551 9.367 27377 Z= 0.268 Chirality : 0.038 0.130 3255 Planarity : 0.004 0.042 3178 Dihedral : 10.817 92.907 3353 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.39 % Allowed : 16.02 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.18), residues: 2380 helix: 2.02 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.09 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 29 TYR 0.009 0.001 TYR E 345 PHE 0.009 0.001 PHE A 54 TRP 0.009 0.001 TRP A 104 HIS 0.002 0.001 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (20146) covalent geometry : angle 0.55022 / 0.27 (27328) SS BOND : bond 0.00279 / 0.19 ( 14) SS BOND : angle 0.63215 / 0.45 ( 28) hydrogen bonds : bond 0.03215 / 2.13 ( 1226) hydrogen bonds : angle 3.65060 / 2.60 ( 3531) link_NAG-ASN : bond 0.00431 / 0.28 ( 7) link_NAG-ASN : angle 1.17694 / 0.82 ( 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 205 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.814 Fit side-chains REVERT: A 9 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: A 56 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8564 (pp30) REVERT: A 254 ARG cc_start: 0.8955 (tpp80) cc_final: 0.8672 (tpp80) REVERT: A 336 GLU cc_start: 0.8898 (tt0) cc_final: 0.8621 (tt0) REVERT: A 337 GLU cc_start: 0.8637 (tp30) cc_final: 0.8343 (tm-30) REVERT: A 352 GLU cc_start: 0.9072 (tp30) cc_final: 0.8748 (tm-30) REVERT: B 9 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: B 31 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8345 (tt0) REVERT: B 254 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8648 (tpp80) REVERT: B 337 GLU cc_start: 0.8771 (tp30) cc_final: 0.8507 (tm-30) REVERT: B 352 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8855 (tm-30) REVERT: C 5 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 9 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: C 29 ARG cc_start: 0.8509 (mmt90) cc_final: 0.8104 (mmm-85) REVERT: C 56 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8448 (pp30) REVERT: C 89 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8662 (mm-40) REVERT: C 261 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8878 (t0) REVERT: C 337 GLU cc_start: 0.8830 (tp30) cc_final: 0.8567 (tp30) REVERT: D 9 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 29 ARG cc_start: 0.8521 (mmt90) cc_final: 0.8238 (mmt90) REVERT: D 56 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8435 (tm-30) REVERT: D 254 ARG cc_start: 0.8670 (tpp80) cc_final: 0.8402 (tpp80) REVERT: D 352 GLU cc_start: 0.9074 (tp30) cc_final: 0.8618 (tm-30) REVERT: E 5 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8392 (tm-30) REVERT: E 9 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: E 56 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8527 (pp30) REVERT: E 254 ARG cc_start: 0.9032 (tpp80) cc_final: 0.8748 (tpp80) REVERT: E 337 GLU cc_start: 0.8694 (tp30) cc_final: 0.8151 (tm-30) REVERT: E 352 GLU cc_start: 0.9150 (tp30) cc_final: 0.8807 (tm-30) REVERT: F 5 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8445 (tm-30) REVERT: F 9 GLU cc_start: 0.8793 (tt0) cc_final: 0.8541 (tm-30) REVERT: F 31 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8411 (tt0) REVERT: F 337 GLU cc_start: 0.8703 (tp30) cc_final: 0.8129 (tm-30) REVERT: G 5 GLN cc_start: 0.8792 (mt0) cc_final: 0.8572 (tm-30) REVERT: G 9 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: G 56 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8571 (pp30) REVERT: G 254 ARG cc_start: 0.8701 (tpp80) cc_final: 0.8461 (tpp80) REVERT: G 261 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8816 (t0) REVERT: G 337 GLU cc_start: 0.8652 (tp30) cc_final: 0.8414 (tm-30) outliers start: 44 outliers final: 21 residues processed: 190 average time/residue: 0.6749 time to fit residues: 143.6790 Evaluate side-chains 185 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 89 GLN Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 261 ASP 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 38 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN F 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.082749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063036 restraints weight = 47192.595| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.47 r_work: 0.2881 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20167 Z= 0.175 Angle : 0.591 9.109 27377 Z= 0.284 Chirality : 0.039 0.128 3255 Planarity : 0.004 0.042 3178 Dihedral : 10.877 91.792 3353 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.77 % Allowed : 16.30 % Favored : 80.93 % 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: 1.20 (0.18), residues: 2380 helix: 1.99 (0.14), residues: 1631 sheet: None (None), residues: 0 loop : -2.04 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 29 TYR 0.010 0.001 TYR B 10 PHE 0.012 0.001 PHE C 54 TRP 0.006 0.001 TRP D 74 HIS 0.001 0.000 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (20146) covalent geometry : angle 0.59051 / 0.28 (27328) SS BOND : bond 0.00430 / 0.29 ( 14) SS BOND : angle 0.86014 / 0.61 ( 28) hydrogen bonds : bond 0.03470 / 2.29 ( 1226) hydrogen bonds : angle 3.72792 / 2.66 ( 3531) link_NAG-ASN : bond 0.00350 / 0.23 ( 7) link_NAG-ASN : angle 1.07065 / 0.74 ( 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 207 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.720 Fit side-chains REVERT: A 9 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: A 56 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8622 (pp30) REVERT: A 254 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8633 (tpp80) REVERT: A 336 GLU cc_start: 0.8924 (tt0) cc_final: 0.8665 (tt0) REVERT: A 337 GLU cc_start: 0.8631 (tp30) cc_final: 0.8305 (tm-30) REVERT: B 9 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: B 31 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8350 (tt0) REVERT: B 254 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8653 (tpp80) REVERT: B 337 GLU cc_start: 0.8782 (tp30) cc_final: 0.8473 (tm-30) REVERT: B 352 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8872 (tm-30) REVERT: C 5 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8432 (tm-30) REVERT: C 9 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: C 29 ARG cc_start: 0.8581 (mmt90) cc_final: 0.8112 (mmm-85) REVERT: C 337 GLU cc_start: 0.8815 (tp30) cc_final: 0.8563 (tp30) REVERT: D 9 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: D 337 GLU cc_start: 0.8722 (tp30) cc_final: 0.7981 (tm-30) REVERT: E 5 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8340 (tm-30) REVERT: E 9 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: E 337 GLU cc_start: 0.8669 (tp30) cc_final: 0.8046 (tm-30) REVERT: F 5 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8507 (tm-30) REVERT: F 9 GLU cc_start: 0.8802 (tt0) cc_final: 0.8484 (tm-30) REVERT: F 31 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8491 (tt0) REVERT: F 337 GLU cc_start: 0.8702 (tp30) cc_final: 0.8141 (tm-30) REVERT: G 5 GLN cc_start: 0.8804 (mt0) cc_final: 0.8573 (tm-30) REVERT: G 9 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: G 254 ARG cc_start: 0.8717 (tpp80) cc_final: 0.8473 (tpp80) REVERT: G 337 GLU cc_start: 0.8697 (tp30) cc_final: 0.8379 (tm-30) outliers start: 51 outliers final: 23 residues processed: 193 average time/residue: 0.6812 time to fit residues: 147.4753 Evaluate side-chains 182 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 9 GLU 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 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 31 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR 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: 0.6980 chunk 137 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 210 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3542 r_free = 0.3542 target = 0.084214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064884 restraints weight = 47091.448| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.48 r_work: 0.2931 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20167 Z= 0.120 Angle : 0.558 7.600 27377 Z= 0.271 Chirality : 0.038 0.131 3255 Planarity : 0.004 0.042 3178 Dihedral : 10.523 90.897 3353 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.85 % Allowed : 17.71 % Favored : 80.45 % 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: 1.32 (0.19), residues: 2380 helix: 2.08 (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 G 29 TYR 0.009 0.001 TYR B 345 PHE 0.010 0.001 PHE D 54 TRP 0.008 0.001 TRP C 104 HIS 0.001 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (20146) covalent geometry : angle 0.55687 / 0.27 (27328) SS BOND : bond 0.00258 / 0.17 ( 14) SS BOND : angle 0.64732 / 0.46 ( 28) hydrogen bonds : bond 0.03185 / 2.11 ( 1226) hydrogen bonds : angle 3.65242 / 2.60 ( 3531) link_NAG-ASN : bond 0.00398 / 0.25 ( 7) link_NAG-ASN : angle 1.07322 / 0.74 ( 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 193 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.764 Fit side-chains REVERT: A 9 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: A 56 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8565 (pp30) REVERT: A 254 ARG cc_start: 0.8962 (tpp80) cc_final: 0.8698 (tpp80) REVERT: A 336 GLU cc_start: 0.8902 (tt0) cc_final: 0.8622 (tt0) REVERT: A 337 GLU cc_start: 0.8620 (tp30) cc_final: 0.8313 (tm-30) REVERT: A 352 GLU cc_start: 0.9110 (tp30) cc_final: 0.8793 (tm-30) REVERT: B 9 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: B 31 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8333 (tt0) REVERT: B 254 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8626 (tpp80) REVERT: B 337 GLU cc_start: 0.8755 (tp30) cc_final: 0.8478 (tm-30) REVERT: B 352 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8869 (tm-30) REVERT: C 5 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8437 (tm-30) REVERT: C 9 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: C 29 ARG cc_start: 0.8478 (mmt90) cc_final: 0.8074 (mmm-85) REVERT: C 337 GLU cc_start: 0.8830 (tp30) cc_final: 0.8555 (tp30) REVERT: D 9 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: D 56 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8514 (pp30) REVERT: D 254 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8471 (tpp80) REVERT: D 352 GLU cc_start: 0.9070 (tp30) cc_final: 0.8665 (tm-30) REVERT: E 5 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8419 (tm-30) REVERT: E 9 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8186 (tm-30) REVERT: E 56 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8478 (pp30) REVERT: E 57 GLU cc_start: 0.8683 (pm20) cc_final: 0.8248 (pm20) REVERT: E 337 GLU cc_start: 0.8667 (tp30) cc_final: 0.8121 (tm-30) REVERT: E 352 GLU cc_start: 0.9172 (tp30) cc_final: 0.8834 (tm-30) REVERT: F 5 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8480 (tm-30) REVERT: F 9 GLU cc_start: 0.8799 (tt0) cc_final: 0.8518 (tm-30) REVERT: F 31 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8389 (tt0) REVERT: F 336 GLU cc_start: 0.9153 (tt0) cc_final: 0.8938 (pt0) REVERT: F 337 GLU cc_start: 0.8699 (tp30) cc_final: 0.8137 (tm-30) REVERT: G 5 GLN cc_start: 0.8781 (mt0) cc_final: 0.8569 (tm-30) REVERT: G 9 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8242 (tm-30) REVERT: G 56 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8559 (pp30) REVERT: G 254 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8471 (tpp80) REVERT: G 337 GLU cc_start: 0.8679 (tp30) cc_final: 0.8427 (tm-30) outliers start: 34 outliers final: 20 residues processed: 183 average time/residue: 0.6884 time to fit residues: 141.0915 Evaluate side-chains 179 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 258 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 9 GLU 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 224 ILE 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 246 CYS Chi-restraints excluded: chain G residue 258 THR 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: 3.9990 chunk 139 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 5 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3529 r_free = 0.3529 target = 0.083617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.064234 restraints weight = 46970.872| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.44 r_work: 0.2921 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20167 Z= 0.134 Angle : 0.564 7.601 27377 Z= 0.274 Chirality : 0.038 0.132 3255 Planarity : 0.004 0.042 3178 Dihedral : 10.428 89.624 3353 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.06 % Allowed : 17.71 % Favored : 80.23 % 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: 1.35 (0.18), residues: 2380 helix: 2.10 (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 G 29 TYR 0.009 0.001 TYR D 345 PHE 0.011 0.001 PHE F 54 TRP 0.008 0.001 TRP E 104 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (20146) covalent geometry : angle 0.56348 / 0.27 (27328) SS BOND : bond 0.00324 / 0.22 ( 14) SS BOND : angle 0.70981 / 0.50 ( 28) hydrogen bonds : bond 0.03249 / 2.15 ( 1226) hydrogen bonds : angle 3.66011 / 2.61 ( 3531) link_NAG-ASN : bond 0.00372 / 0.24 ( 7) link_NAG-ASN : angle 1.01812 / 0.70 ( 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 195 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.799 Fit side-chains REVERT: A 9 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: A 56 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8598 (pp30) REVERT: A 254 ARG cc_start: 0.8960 (tpp80) cc_final: 0.8695 (tpp80) REVERT: A 336 GLU cc_start: 0.8883 (tt0) cc_final: 0.8589 (tt0) REVERT: A 352 GLU cc_start: 0.9082 (tp30) cc_final: 0.8811 (tm-30) REVERT: B 9 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: B 31 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8325 (tt0) REVERT: B 254 ARG cc_start: 0.8871 (tpp80) cc_final: 0.8641 (tpp80) REVERT: B 352 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8868 (tm-30) REVERT: C 5 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8468 (tm-30) REVERT: C 9 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: C 29 ARG cc_start: 0.8513 (mmt90) cc_final: 0.8057 (mmm-85) REVERT: C 56 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8285 (pp30) REVERT: C 89 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8663 (mm-40) REVERT: C 337 GLU cc_start: 0.8813 (tp30) cc_final: 0.8534 (tp30) REVERT: C 352 GLU cc_start: 0.9109 (tp30) cc_final: 0.8815 (tm-30) REVERT: D 9 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: D 56 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8532 (pp30) REVERT: D 254 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8516 (tpp80) REVERT: D 337 GLU cc_start: 0.8636 (tp30) cc_final: 0.7857 (tm-30) REVERT: D 352 GLU cc_start: 0.9065 (tp30) cc_final: 0.8690 (tm-30) REVERT: E 5 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8425 (tm-30) REVERT: E 9 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: E 56 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8504 (pp30) REVERT: E 57 GLU cc_start: 0.8673 (pm20) cc_final: 0.8219 (pm20) REVERT: E 337 GLU cc_start: 0.8651 (tp30) cc_final: 0.8115 (tm-30) REVERT: E 352 GLU cc_start: 0.9149 (tp30) cc_final: 0.8874 (tm-30) REVERT: F 5 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8540 (tm-30) REVERT: F 9 GLU cc_start: 0.8835 (tt0) cc_final: 0.8511 (tm-30) REVERT: F 337 GLU cc_start: 0.8703 (tp30) cc_final: 0.8139 (tm-30) REVERT: F 352 GLU cc_start: 0.9129 (tp30) cc_final: 0.8875 (tm-30) REVERT: G 9 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8186 (tm-30) REVERT: G 56 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8594 (pp30) REVERT: G 254 ARG cc_start: 0.8709 (tpp80) cc_final: 0.8478 (tpp80) REVERT: G 337 GLU cc_start: 0.8669 (tp30) cc_final: 0.8423 (tm-30) REVERT: G 352 GLU cc_start: 0.9064 (tp30) cc_final: 0.8827 (tm-30) outliers start: 38 outliers final: 24 residues processed: 184 average time/residue: 0.6989 time to fit residues: 144.0224 Evaluate side-chains 184 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 38 VAL 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 9 GLU Chi-restraints excluded: chain C residue 89 GLN 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 308 VAL Chi-restraints excluded: chain D residue 9 GLU 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 9 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 224 ILE 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 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR 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: 20.0000 chunk 80 optimal weight: 0.9980 chunk 137 optimal weight: 0.0030 chunk 124 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN E 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.083703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.064292 restraints weight = 47095.364| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.45 r_work: 0.2922 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2677 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= 0.135 Angle : 0.571 7.865 27377 Z= 0.277 Chirality : 0.038 0.130 3255 Planarity : 0.004 0.043 3178 Dihedral : 10.366 88.793 3353 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.68 % Allowed : 17.93 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.19), residues: 2380 helix: 2.31 (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 0.010 0.001 ARG G 29 TYR 0.009 0.001 TYR D 345 PHE 0.011 0.001 PHE A 54 TRP 0.007 0.001 TRP E 104 HIS 0.001 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (20146) covalent geometry : angle 0.57061 / 0.28 (27328) SS BOND : bond 0.00314 / 0.21 ( 14) SS BOND : angle 0.70459 / 0.50 ( 28) hydrogen bonds : bond 0.03237 / 2.15 ( 1226) hydrogen bonds : angle 3.67759 / 2.62 ( 3531) link_NAG-ASN : bond 0.00372 / 0.24 ( 7) link_NAG-ASN : angle 0.98255 / 0.68 ( 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 187 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 3.016 Fit side-chains REVERT: A 9 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: A 56 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8611 (pp30) REVERT: A 254 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8692 (tpp80) REVERT: A 336 GLU cc_start: 0.8808 (tt0) cc_final: 0.8581 (tt0) REVERT: A 352 GLU cc_start: 0.9104 (tp30) cc_final: 0.8823 (tm-30) REVERT: B 9 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: B 254 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8648 (tpp80) REVERT: B 337 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 352 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8873 (tm-30) REVERT: C 5 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8477 (tm-30) REVERT: C 9 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8107 (tm-30) REVERT: C 29 ARG cc_start: 0.8487 (mmt90) cc_final: 0.8061 (mmm-85) REVERT: C 56 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8370 (pp30) REVERT: C 337 GLU cc_start: 0.8820 (tp30) cc_final: 0.8590 (tp30) REVERT: C 352 GLU cc_start: 0.9125 (tp30) cc_final: 0.8827 (tm-30) REVERT: D 9 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: D 56 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8531 (pp30) REVERT: D 254 ARG cc_start: 0.8791 (tpp80) cc_final: 0.8523 (tpp80) REVERT: D 337 GLU cc_start: 0.8670 (tp30) cc_final: 0.8021 (tm-30) REVERT: D 352 GLU cc_start: 0.9077 (tp30) cc_final: 0.8753 (tm-30) REVERT: E 5 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8484 (tm-30) REVERT: E 9 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: E 337 GLU cc_start: 0.8652 (tp30) cc_final: 0.8120 (tm-30) REVERT: E 352 GLU cc_start: 0.9158 (tp30) cc_final: 0.8902 (tm-30) REVERT: F 5 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8526 (tm-30) REVERT: F 9 GLU cc_start: 0.8820 (tt0) cc_final: 0.8557 (tm-30) REVERT: F 337 GLU cc_start: 0.8711 (tp30) cc_final: 0.8161 (tm-30) REVERT: F 352 GLU cc_start: 0.9138 (tp30) cc_final: 0.8883 (tm-30) REVERT: G 9 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8241 (tm-30) REVERT: G 56 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8492 (pp30) REVERT: G 254 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8480 (tpp80) REVERT: G 337 GLU cc_start: 0.8654 (tp30) cc_final: 0.8416 (tm-30) REVERT: G 352 GLU cc_start: 0.9084 (tp30) cc_final: 0.8854 (tm-30) outliers start: 31 outliers final: 21 residues processed: 177 average time/residue: 0.6690 time to fit residues: 132.8977 Evaluate side-chains 180 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 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 258 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 9 GLU 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 9 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 224 ILE 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 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 258 THR 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: 0.6980 chunk 164 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN C 89 GLN E 89 GLN G 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.085050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.065822 restraints weight = 47133.849| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.51 r_work: 0.2963 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2929 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= 0.110 Angle : 0.553 7.592 27377 Z= 0.269 Chirality : 0.038 0.130 3255 Planarity : 0.004 0.044 3178 Dihedral : 9.970 87.056 3353 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.36 % Allowed : 18.31 % 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: 1.49 (0.19), residues: 2380 helix: 2.18 (0.14), residues: 1638 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 29 TYR 0.009 0.001 TYR D 345 PHE 0.009 0.001 PHE A 54 TRP 0.009 0.001 TRP D 104 HIS 0.001 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (20146) covalent geometry : angle 0.55308 / 0.27 (27328) SS BOND : bond 0.00205 / 0.14 ( 14) SS BOND : angle 0.49926 / 0.35 ( 28) hydrogen bonds : bond 0.03020 / 2.00 ( 1226) hydrogen bonds : angle 3.60684 / 2.57 ( 3531) link_NAG-ASN : bond 0.00391 / 0.25 ( 7) link_NAG-ASN : angle 0.99641 / 0.69 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4618.30 seconds wall clock time: 80 minutes 13.71 seconds (4813.71 seconds total)