Starting phenix.real_space_refine on Sat Mar 7 10:13:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfe_25871/03_2026/7tfe_25871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfe_25871/03_2026/7tfe_25871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tfe_25871/03_2026/7tfe_25871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfe_25871/03_2026/7tfe_25871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tfe_25871/03_2026/7tfe_25871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfe_25871/03_2026/7tfe_25871.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 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 Mg 24 5.21 5 S 216 5.16 5 C 26592 2.51 5 N 6948 2.21 5 O 7608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41388 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "H" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "I" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "F" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "K" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "L" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU A 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU A 350 " occ=0.92 residue: pdb=" N LEU G 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU G 350 " occ=0.92 residue: pdb=" N LEU H 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU H 350 " occ=0.92 residue: pdb=" N LEU I 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU I 350 " occ=0.92 residue: pdb=" N LEU B 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU B 350 " occ=0.92 residue: pdb=" N LEU C 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU C 350 " occ=0.92 residue: pdb=" N LEU J 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU J 350 " occ=0.92 residue: pdb=" N LEU D 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU D 350 " occ=0.92 residue: pdb=" N LEU E 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU E 350 " occ=0.92 residue: pdb=" N LEU F 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU F 350 " occ=0.92 residue: pdb=" N LEU K 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU K 350 " occ=0.92 residue: pdb=" N LEU L 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU L 350 " occ=0.92 Time building chain proxies: 9.68, per 1000 atoms: 0.23 Number of scatterers: 41388 At special positions: 0 Unit cell: (159.28, 152.24, 122.32, 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 216 16.00 Mg 24 11.99 O 7608 8.00 N 6948 7.00 C 26592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.9 seconds 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9912 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 72 sheets defined 46.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 62 " --> pdb=" O GLY A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 62' Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 361 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 41 through 47 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG G 62 " --> pdb=" O GLY G 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 62' Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR G 76 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 123 Processing helix chain 'G' and resid 167 through 180 Processing helix chain 'G' and resid 203 through 225 Processing helix chain 'G' and resid 263 through 267 Processing helix chain 'G' and resid 268 through 281 Processing helix chain 'G' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA G 287 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL G 288 " --> pdb=" O GLY G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 299' Processing helix chain 'G' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER G 329 " --> pdb=" O ARG G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 361 Processing helix chain 'G' and resid 376 through 383 Processing helix chain 'G' and resid 391 through 402 Processing helix chain 'G' and resid 403 through 410 Processing helix chain 'G' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE G 414 " --> pdb=" O GLY G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG G 437 " --> pdb=" O HIS G 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 16 Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 58 through 62 removed outlier: 4.165A pdb=" N VAL H 61 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG H 62 " --> pdb=" O GLY H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 62' Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.616A pdb=" N THR H 76 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 Processing helix chain 'H' and resid 167 through 180 Processing helix chain 'H' and resid 203 through 225 Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 281 Processing helix chain 'H' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA H 287 " --> pdb=" O ARG H 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL H 288 " --> pdb=" O GLY H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 299 removed outlier: 4.036A pdb=" N PHE H 296 " --> pdb=" O THR H 292 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS H 297 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 299 " --> pdb=" O SER H 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 292 through 299' Processing helix chain 'H' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER H 329 " --> pdb=" O ARG H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 361 Processing helix chain 'H' and resid 376 through 383 Processing helix chain 'H' and resid 391 through 402 Processing helix chain 'H' and resid 403 through 410 Processing helix chain 'H' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE H 414 " --> pdb=" O GLY H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG H 437 " --> pdb=" O HIS H 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 16 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'I' and resid 58 through 62 removed outlier: 4.165A pdb=" N VAL I 61 " --> pdb=" O GLU I 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG I 62 " --> pdb=" O GLY I 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 58 through 62' Processing helix chain 'I' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR I 76 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 123 Processing helix chain 'I' and resid 167 through 180 Processing helix chain 'I' and resid 203 through 225 Processing helix chain 'I' and resid 263 through 267 Processing helix chain 'I' and resid 268 through 281 Processing helix chain 'I' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA I 287 " --> pdb=" O ARG I 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL I 288 " --> pdb=" O GLY I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 299 " --> pdb=" O SER I 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 294 through 299' Processing helix chain 'I' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER I 329 " --> pdb=" O ARG I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 361 Processing helix chain 'I' and resid 376 through 383 Processing helix chain 'I' and resid 391 through 402 Processing helix chain 'I' and resid 403 through 410 Processing helix chain 'I' and resid 410 through 431 removed outlier: 3.550A pdb=" N PHE I 414 " --> pdb=" O GLY I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG I 437 " --> pdb=" O HIS I 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 16 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 62 " --> pdb=" O GLY B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 62' Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.616A pdb=" N THR B 76 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 203 through 225 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 281 through 290 removed outlier: 4.960A pdb=" N ALA B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.628A pdb=" N SER B 329 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 361 Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.620A pdb=" N ARG B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 62' Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.616A pdb=" N THR C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 203 through 225 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 294 through 299' Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER C 329 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 361 Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 391 through 402 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.646A pdb=" N ARG C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 16 Processing helix chain 'J' and resid 41 through 47 Processing helix chain 'J' and resid 55 through 57 No H-bonds generated for 'chain 'J' and resid 55 through 57' Processing helix chain 'J' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL J 61 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG J 62 " --> pdb=" O GLY J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'J' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR J 76 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 123 Processing helix chain 'J' and resid 167 through 180 Processing helix chain 'J' and resid 203 through 225 Processing helix chain 'J' and resid 263 through 267 Processing helix chain 'J' and resid 268 through 281 Processing helix chain 'J' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA J 287 " --> pdb=" O ARG J 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL J 288 " --> pdb=" O GLY J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG J 298 " --> pdb=" O ASN J 294 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 299 " --> pdb=" O SER J 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 294 through 299' Processing helix chain 'J' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER J 329 " --> pdb=" O ARG J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 360 Processing helix chain 'J' and resid 376 through 383 Processing helix chain 'J' and resid 391 through 402 Processing helix chain 'J' and resid 403 through 410 Processing helix chain 'J' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE J 414 " --> pdb=" O GLY J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG J 437 " --> pdb=" O HIS J 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 16 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 62 " --> pdb=" O GLY D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 62' Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR D 76 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 203 through 225 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 4.043A pdb=" N PHE D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 292 through 299' Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER D 329 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 361 Processing helix chain 'D' and resid 376 through 383 Processing helix chain 'D' and resid 391 through 402 Processing helix chain 'D' and resid 403 through 410 Processing helix chain 'D' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE D 414 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL E 61 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 62 " --> pdb=" O GLY E 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 62' Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR E 76 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 123 Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 203 through 225 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 281 through 290 removed outlier: 4.960A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 299 removed outlier: 4.035A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 299 " --> pdb=" O SER E 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 299' Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER E 329 " --> pdb=" O ARG E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 361 Processing helix chain 'E' and resid 376 through 383 Processing helix chain 'E' and resid 391 through 402 Processing helix chain 'E' and resid 403 through 410 Processing helix chain 'E' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE E 414 " --> pdb=" O GLY E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL F 61 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 62 " --> pdb=" O GLY F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 62' Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.616A pdb=" N THR F 76 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 203 through 225 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 281 through 290 removed outlier: 4.960A pdb=" N ALA F 287 " --> pdb=" O ARG F 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 294 through 299' Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER F 329 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 361 Processing helix chain 'F' and resid 376 through 383 Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 403 through 410 Processing helix chain 'F' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE F 414 " --> pdb=" O GLY F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 16 Processing helix chain 'K' and resid 41 through 47 Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 58 through 62 removed outlier: 4.165A pdb=" N VAL K 61 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG K 62 " --> pdb=" O GLY K 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 62' Processing helix chain 'K' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR K 76 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 123 Processing helix chain 'K' and resid 167 through 180 Processing helix chain 'K' and resid 203 through 225 Processing helix chain 'K' and resid 263 through 267 Processing helix chain 'K' and resid 268 through 281 Processing helix chain 'K' and resid 281 through 290 removed outlier: 4.960A pdb=" N ALA K 287 " --> pdb=" O ARG K 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL K 288 " --> pdb=" O GLY K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG K 298 " --> pdb=" O ASN K 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU K 299 " --> pdb=" O SER K 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 294 through 299' Processing helix chain 'K' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER K 329 " --> pdb=" O ARG K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 361 Processing helix chain 'K' and resid 376 through 383 Processing helix chain 'K' and resid 391 through 402 Processing helix chain 'K' and resid 403 through 410 Processing helix chain 'K' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE K 414 " --> pdb=" O GLY K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 441 removed outlier: 3.628A pdb=" N ARG K 437 " --> pdb=" O HIS K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 16 Processing helix chain 'L' and resid 41 through 47 Processing helix chain 'L' and resid 55 through 57 No H-bonds generated for 'chain 'L' and resid 55 through 57' Processing helix chain 'L' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL L 61 " --> pdb=" O GLU L 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG L 62 " --> pdb=" O GLY L 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 58 through 62' Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR L 76 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 123 Processing helix chain 'L' and resid 167 through 180 Processing helix chain 'L' and resid 203 through 225 Processing helix chain 'L' and resid 263 through 267 Processing helix chain 'L' and resid 268 through 281 Processing helix chain 'L' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA L 287 " --> pdb=" O ARG L 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL L 288 " --> pdb=" O GLY L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG L 298 " --> pdb=" O ASN L 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU L 299 " --> pdb=" O SER L 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 294 through 299' Processing helix chain 'L' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER L 329 " --> pdb=" O ARG L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 361 Processing helix chain 'L' and resid 376 through 383 Processing helix chain 'L' and resid 391 through 402 Processing helix chain 'L' and resid 403 through 410 Processing helix chain 'L' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE L 414 " --> pdb=" O GLY L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG L 437 " --> pdb=" O HIS L 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS A 88 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A 89 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 132 removed outlier: 3.675A pdb=" N GLU A 126 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS A 245 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 185 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS G 88 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL G 89 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'G' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 126 through 132 removed outlier: 3.675A pdb=" N GLU G 126 " --> pdb=" O PHE G 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS G 245 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA G 185 " --> pdb=" O ASP G 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS H 88 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL H 89 " --> pdb=" O PHE H 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AB6, first strand: chain 'H' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR H 102 " --> pdb=" O ASN H 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU H 126 " --> pdb=" O PHE H 251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS H 245 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU H 149 " --> pdb=" O LYS H 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA H 185 " --> pdb=" O ASP H 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU H 149 " --> pdb=" O LYS H 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS I 88 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL I 89 " --> pdb=" O PHE I 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AC3, first strand: chain 'I' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 126 through 132 removed outlier: 3.675A pdb=" N GLU I 126 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS I 245 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU I 149 " --> pdb=" O LYS I 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA I 185 " --> pdb=" O ASP I 198 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU I 149 " --> pdb=" O LYS I 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS B 88 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AC9, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 126 through 132 removed outlier: 3.675A pdb=" N GLU B 126 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS B 245 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU B 149 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 185 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU B 149 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS C 88 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C 89 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD6, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU C 126 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS C 245 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU C 149 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 185 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU C 149 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS J 88 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL J 89 " --> pdb=" O PHE J 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 51 through 53 Processing sheet with id=AE3, first strand: chain 'J' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU J 126 " --> pdb=" O PHE J 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS J 245 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU J 149 " --> pdb=" O LYS J 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA J 185 " --> pdb=" O ASP J 198 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU J 149 " --> pdb=" O LYS J 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS D 88 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL D 89 " --> pdb=" O PHE D 80 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE9, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU D 126 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS D 245 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU D 149 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 185 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU D 149 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS E 88 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 89 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AF6, first strand: chain 'E' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU E 126 " --> pdb=" O PHE E 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS E 245 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU E 149 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA E 185 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU E 149 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS F 88 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL F 89 " --> pdb=" O PHE F 80 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AG3, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU F 126 " --> pdb=" O PHE F 251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS F 245 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU F 149 " --> pdb=" O LYS F 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA F 185 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU F 149 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS K 88 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL K 89 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 51 through 53 Processing sheet with id=AG9, first strand: chain 'K' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU K 126 " --> pdb=" O PHE K 251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS K 245 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU K 149 " --> pdb=" O LYS K 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA K 185 " --> pdb=" O ASP K 198 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU K 149 " --> pdb=" O LYS K 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS L 88 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL L 89 " --> pdb=" O PHE L 80 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 51 through 53 Processing sheet with id=AH6, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR L 102 " --> pdb=" O ASN L 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU L 126 " --> pdb=" O PHE L 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS L 245 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU L 149 " --> pdb=" O LYS L 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA L 185 " --> pdb=" O ASP L 198 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU L 149 " --> pdb=" O LYS L 139 " (cutoff:3.500A) 1979 hydrogen bonds defined for protein. 5721 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: 10.00 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10940 1.33 - 1.45: 7687 1.45 - 1.57: 23397 1.57 - 1.69: 0 1.69 - 1.81: 372 Bond restraints: 42396 Sorted by residual: bond pdb=" N THR H 292 " pdb=" CA THR H 292 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N THR D 292 " pdb=" CA THR D 292 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.18e-02 7.18e+03 1.00e+01 bond pdb=" N THR E 292 " pdb=" CA THR E 292 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.18e-02 7.18e+03 9.80e+00 bond pdb=" N ILE I 358 " pdb=" CA ILE I 358 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 8.95e+00 bond pdb=" N ILE B 221 " pdb=" CA ILE B 221 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.92e+00 ... (remaining 42391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 53757 1.24 - 2.49: 2774 2.49 - 3.73: 835 3.73 - 4.97: 86 4.97 - 6.22: 52 Bond angle restraints: 57504 Sorted by residual: angle pdb=" CA ILE E 418 " pdb=" C ILE E 418 " pdb=" O ILE E 418 " ideal model delta sigma weight residual 121.27 117.64 3.63 1.04e+00 9.25e-01 1.22e+01 angle pdb=" CA ILE A 418 " pdb=" C ILE A 418 " pdb=" O ILE A 418 " ideal model delta sigma weight residual 121.27 117.70 3.57 1.04e+00 9.25e-01 1.18e+01 angle pdb=" CA ILE C 418 " pdb=" C ILE C 418 " pdb=" O ILE C 418 " ideal model delta sigma weight residual 121.27 117.71 3.56 1.04e+00 9.25e-01 1.17e+01 angle pdb=" CA ILE I 418 " pdb=" C ILE I 418 " pdb=" O ILE I 418 " ideal model delta sigma weight residual 121.27 117.71 3.56 1.04e+00 9.25e-01 1.17e+01 angle pdb=" N TYR J 373 " pdb=" CA TYR J 373 " pdb=" C TYR J 373 " ideal model delta sigma weight residual 114.75 110.64 4.11 1.26e+00 6.30e-01 1.06e+01 ... (remaining 57499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 23089 17.97 - 35.95: 1643 35.95 - 53.92: 461 53.92 - 71.89: 90 71.89 - 89.87: 49 Dihedral angle restraints: 25332 sinusoidal: 9948 harmonic: 15384 Sorted by residual: dihedral pdb=" CA GLU L 15 " pdb=" C GLU L 15 " pdb=" N GLN L 16 " pdb=" CA GLN L 16 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CA GLU F 15 " pdb=" C GLU F 15 " pdb=" N GLN F 16 " pdb=" CA GLN F 16 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.84e+00 dihedral pdb=" CA GLU K 15 " pdb=" C GLU K 15 " pdb=" N GLN K 16 " pdb=" CA GLN K 16 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.84e+00 ... (remaining 25329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4593 0.045 - 0.089: 1082 0.089 - 0.134: 540 0.134 - 0.179: 75 0.179 - 0.223: 10 Chirality restraints: 6300 Sorted by residual: chirality pdb=" CA ILE E 293 " pdb=" N ILE E 293 " pdb=" C ILE E 293 " pdb=" CB ILE E 293 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE H 293 " pdb=" N ILE H 293 " pdb=" C ILE H 293 " pdb=" CB ILE H 293 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE D 293 " pdb=" N ILE D 293 " pdb=" C ILE D 293 " pdb=" CB ILE D 293 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 6297 not shown) Planarity restraints: 7512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 244 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C MET A 244 " -0.025 2.00e-02 2.50e+03 pdb=" O MET A 244 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS A 245 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 244 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C MET I 244 " -0.025 2.00e-02 2.50e+03 pdb=" O MET I 244 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS I 245 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 244 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C MET C 244 " -0.025 2.00e-02 2.50e+03 pdb=" O MET C 244 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS C 245 " 0.008 2.00e-02 2.50e+03 ... (remaining 7509 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 592 2.65 - 3.21: 38398 3.21 - 3.77: 65063 3.77 - 4.34: 92844 4.34 - 4.90: 154434 Nonbonded interactions: 351331 Sorted by model distance: nonbonded pdb=" OE2 GLU I 333 " pdb="MG MG I 502 " model vdw 2.083 2.170 nonbonded pdb=" OE2 GLU J 333 " pdb="MG MG J 502 " model vdw 2.083 2.170 nonbonded pdb=" OE2 GLU A 333 " pdb="MG MG A 502 " model vdw 2.083 2.170 nonbonded pdb=" OE2 GLU C 333 " pdb="MG MG C 502 " model vdw 2.083 2.170 nonbonded pdb=" OE2 GLU G 333 " pdb="MG MG G 502 " model vdw 2.084 2.170 ... (remaining 351326 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'L' } 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=0.92 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: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 40.660 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.120 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 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 : 0.004 0.038 42396 Z= 0.291 Angle : 0.675 6.218 57504 Z= 0.448 Chirality : 0.048 0.223 6300 Planarity : 0.004 0.034 7512 Dihedral : 14.579 89.866 15420 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.18 % Allowed : 1.87 % Favored : 95.95 % 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: 0.27 (0.12), residues: 5292 helix: 1.41 (0.11), residues: 2052 sheet: -0.30 (0.18), residues: 900 loop : -0.69 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 169 TYR 0.011 0.001 TYR E 285 PHE 0.010 0.001 PHE G 124 TRP 0.015 0.001 TRP G 435 HIS 0.003 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00417 (42396) covalent geometry : angle 0.67533 (57504) hydrogen bonds : bond 0.15583 ( 1967) hydrogen bonds : angle 6.00436 ( 5721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 938 time to evaluate : 1.860 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.7389 (mmt) cc_final: 0.6992 (tpt) REVERT: A 69 TYR cc_start: 0.6868 (m-80) cc_final: 0.6577 (m-80) REVERT: A 73 ASP cc_start: 0.6510 (t0) cc_final: 0.5227 (m-30) REVERT: A 181 PHE cc_start: 0.4973 (m-10) cc_final: 0.4531 (m-80) REVERT: A 182 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6613 (mt-10) REVERT: A 224 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6997 (pttm) REVERT: A 361 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6023 (mm-30) REVERT: A 386 TYR cc_start: 0.5478 (m-80) cc_final: 0.4852 (m-80) REVERT: A 390 GLU cc_start: 0.6803 (pm20) cc_final: 0.6344 (pm20) REVERT: A 398 GLU cc_start: 0.5829 (mm-30) cc_final: 0.5405 (mm-30) REVERT: G 43 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5681 (mptt) REVERT: G 51 MET cc_start: 0.7459 (mmt) cc_final: 0.7257 (tpt) REVERT: G 67 ASP cc_start: 0.5943 (m-30) cc_final: 0.5574 (p0) REVERT: G 69 TYR cc_start: 0.6877 (m-80) cc_final: 0.6565 (m-80) REVERT: G 73 ASP cc_start: 0.6407 (t0) cc_final: 0.5440 (m-30) REVERT: G 182 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6520 (mt-10) REVERT: G 223 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6032 (tpt90) REVERT: G 361 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6082 (mm-30) REVERT: G 386 TYR cc_start: 0.5238 (m-80) cc_final: 0.4684 (m-80) REVERT: G 390 GLU cc_start: 0.6713 (pm20) cc_final: 0.6209 (pm20) REVERT: H 24 GLN cc_start: 0.5429 (pt0) cc_final: 0.5224 (pt0) REVERT: H 51 MET cc_start: 0.7391 (mmt) cc_final: 0.7044 (tpt) REVERT: H 69 TYR cc_start: 0.7100 (m-80) cc_final: 0.6856 (m-80) REVERT: H 73 ASP cc_start: 0.6576 (t0) cc_final: 0.5409 (m-30) REVERT: H 118 GLU cc_start: 0.5036 (mt-10) cc_final: 0.4715 (tt0) REVERT: H 119 MET cc_start: 0.6552 (ttp) cc_final: 0.6318 (ttp) REVERT: H 181 PHE cc_start: 0.4790 (m-10) cc_final: 0.4342 (m-80) REVERT: H 182 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6629 (mt-10) REVERT: H 223 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6256 (tpt90) REVERT: H 360 ASP cc_start: 0.6494 (m-30) cc_final: 0.6276 (m-30) REVERT: H 361 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6228 (mm-30) REVERT: H 386 TYR cc_start: 0.5524 (m-80) cc_final: 0.4886 (m-80) REVERT: I 7 GLU cc_start: 0.5553 (mp0) cc_final: 0.5057 (mm-30) REVERT: I 51 MET cc_start: 0.7667 (mmt) cc_final: 0.7284 (tpt) REVERT: I 67 ASP cc_start: 0.6267 (m-30) cc_final: 0.5521 (p0) REVERT: I 69 TYR cc_start: 0.6548 (m-80) cc_final: 0.6118 (m-80) REVERT: I 73 ASP cc_start: 0.6306 (t0) cc_final: 0.5387 (m-30) REVERT: I 93 ILE cc_start: 0.6138 (mm) cc_final: 0.5778 (mm) REVERT: I 128 ASN cc_start: 0.7477 (m-40) cc_final: 0.7202 (m110) REVERT: I 181 PHE cc_start: 0.4831 (m-10) cc_final: 0.4405 (m-80) REVERT: I 182 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6486 (mt-10) REVERT: I 223 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6295 (tpt90) REVERT: I 361 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6134 (mm-30) REVERT: I 386 TYR cc_start: 0.5443 (m-80) cc_final: 0.4775 (m-80) REVERT: I 390 GLU cc_start: 0.6829 (pm20) cc_final: 0.6330 (pm20) REVERT: I 398 GLU cc_start: 0.5783 (mm-30) cc_final: 0.5301 (mm-30) REVERT: B 7 GLU cc_start: 0.5946 (mp0) cc_final: 0.5293 (mm-30) REVERT: B 67 ASP cc_start: 0.6128 (m-30) cc_final: 0.5638 (p0) REVERT: B 69 TYR cc_start: 0.6735 (m-80) cc_final: 0.6418 (m-80) REVERT: B 73 ASP cc_start: 0.6448 (t0) cc_final: 0.5518 (m-30) REVERT: B 181 PHE cc_start: 0.4735 (m-10) cc_final: 0.4345 (m-80) REVERT: B 182 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6502 (mt-10) REVERT: B 223 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6156 (tpt170) REVERT: B 361 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6132 (mm-30) REVERT: B 390 GLU cc_start: 0.6597 (pm20) cc_final: 0.6239 (pt0) REVERT: C 7 GLU cc_start: 0.5889 (mp0) cc_final: 0.5390 (mm-30) REVERT: C 43 LYS cc_start: 0.5852 (OUTLIER) cc_final: 0.5645 (mptt) REVERT: C 49 LYS cc_start: 0.6953 (mmmm) cc_final: 0.6572 (mmmt) REVERT: C 67 ASP cc_start: 0.6194 (m-30) cc_final: 0.5683 (p0) REVERT: C 73 ASP cc_start: 0.6449 (t0) cc_final: 0.5447 (m-30) REVERT: C 93 ILE cc_start: 0.6339 (mm) cc_final: 0.6019 (mm) REVERT: C 181 PHE cc_start: 0.4807 (m-10) cc_final: 0.4362 (m-80) REVERT: C 182 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6634 (mt-10) REVERT: C 223 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6175 (tpt90) REVERT: C 240 ASN cc_start: 0.5652 (t0) cc_final: 0.5424 (p0) REVERT: C 386 TYR cc_start: 0.5550 (m-80) cc_final: 0.4812 (m-80) REVERT: C 390 GLU cc_start: 0.6772 (pm20) cc_final: 0.6244 (pm20) REVERT: J 43 LYS cc_start: 0.6441 (ttmm) cc_final: 0.5829 (mptt) REVERT: J 47 ASP cc_start: 0.5817 (m-30) cc_final: 0.5616 (t0) REVERT: J 51 MET cc_start: 0.7573 (mmt) cc_final: 0.7159 (tpt) REVERT: J 73 ASP cc_start: 0.6555 (t0) cc_final: 0.5263 (m-30) REVERT: J 181 PHE cc_start: 0.4681 (m-10) cc_final: 0.4216 (m-80) REVERT: J 182 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6595 (mt-10) REVERT: J 223 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6215 (tpt90) REVERT: J 360 ASP cc_start: 0.6529 (m-30) cc_final: 0.6312 (m-30) REVERT: J 361 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6140 (mm-30) REVERT: J 386 TYR cc_start: 0.5563 (m-80) cc_final: 0.4883 (m-80) REVERT: J 390 GLU cc_start: 0.6819 (pm20) cc_final: 0.6361 (pm20) REVERT: J 398 GLU cc_start: 0.5853 (mm-30) cc_final: 0.5454 (mm-30) REVERT: D 51 MET cc_start: 0.7567 (mmt) cc_final: 0.7359 (tpt) REVERT: D 67 ASP cc_start: 0.6078 (m-30) cc_final: 0.5640 (p0) REVERT: D 69 TYR cc_start: 0.6790 (m-80) cc_final: 0.6517 (m-80) REVERT: D 73 ASP cc_start: 0.6440 (t0) cc_final: 0.5535 (m-30) REVERT: D 93 ILE cc_start: 0.6130 (mm) cc_final: 0.5928 (mm) REVERT: D 181 PHE cc_start: 0.4644 (m-10) cc_final: 0.4248 (m-80) REVERT: D 182 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6417 (mt-10) REVERT: D 223 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6008 (tpt90) REVERT: D 361 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6073 (mm-30) REVERT: D 386 TYR cc_start: 0.5414 (m-80) cc_final: 0.4730 (m-80) REVERT: D 390 GLU cc_start: 0.6723 (pm20) cc_final: 0.6232 (pm20) REVERT: E 51 MET cc_start: 0.7430 (mmt) cc_final: 0.7135 (tpt) REVERT: E 69 TYR cc_start: 0.7008 (m-80) cc_final: 0.6663 (m-80) REVERT: E 73 ASP cc_start: 0.6566 (t0) cc_final: 0.5402 (m-30) REVERT: E 118 GLU cc_start: 0.5150 (mt-10) cc_final: 0.4797 (tt0) REVERT: E 167 ASN cc_start: 0.6342 (t0) cc_final: 0.6134 (t0) REVERT: E 181 PHE cc_start: 0.4735 (m-10) cc_final: 0.4259 (m-80) REVERT: E 182 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6642 (mt-10) REVERT: E 240 ASN cc_start: 0.5602 (t0) cc_final: 0.5270 (p0) REVERT: E 361 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6179 (mm-30) REVERT: E 386 TYR cc_start: 0.5570 (m-80) cc_final: 0.4928 (m-80) REVERT: E 390 GLU cc_start: 0.6781 (pm20) cc_final: 0.6234 (pm20) REVERT: F 7 GLU cc_start: 0.5783 (mp0) cc_final: 0.5213 (mm-30) REVERT: F 51 MET cc_start: 0.7495 (mmt) cc_final: 0.7082 (tpt) REVERT: F 69 TYR cc_start: 0.6611 (m-80) cc_final: 0.6265 (m-80) REVERT: F 73 ASP cc_start: 0.6281 (t0) cc_final: 0.5238 (m-30) REVERT: F 144 ARG cc_start: 0.6621 (mmm160) cc_final: 0.6361 (mmm160) REVERT: F 181 PHE cc_start: 0.4799 (m-10) cc_final: 0.4443 (m-80) REVERT: F 182 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6579 (mt-10) REVERT: F 223 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6139 (tpt90) REVERT: F 361 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6038 (mm-30) REVERT: F 386 TYR cc_start: 0.5327 (m-80) cc_final: 0.4783 (m-80) REVERT: F 390 GLU cc_start: 0.6701 (pm20) cc_final: 0.6336 (pt0) REVERT: F 398 GLU cc_start: 0.5733 (mm-30) cc_final: 0.5301 (mm-30) REVERT: K 49 LYS cc_start: 0.6736 (mmmm) cc_final: 0.6498 (mmmt) REVERT: K 51 MET cc_start: 0.7451 (mmt) cc_final: 0.7242 (tpt) REVERT: K 67 ASP cc_start: 0.5992 (m-30) cc_final: 0.5619 (p0) REVERT: K 73 ASP cc_start: 0.6442 (t0) cc_final: 0.5538 (m-30) REVERT: K 182 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6541 (mt-10) REVERT: K 223 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6030 (tpt90) REVERT: K 240 ASN cc_start: 0.5827 (t0) cc_final: 0.5595 (p0) REVERT: K 361 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6130 (mm-30) REVERT: K 390 GLU cc_start: 0.6747 (pm20) cc_final: 0.6240 (pm20) REVERT: L 7 GLU cc_start: 0.5897 (mp0) cc_final: 0.5375 (mm-30) REVERT: L 43 LYS cc_start: 0.6622 (ttmm) cc_final: 0.5852 (mptt) REVERT: L 47 ASP cc_start: 0.5627 (m-30) cc_final: 0.5331 (t0) REVERT: L 51 MET cc_start: 0.7475 (mmt) cc_final: 0.7184 (tpt) REVERT: L 69 TYR cc_start: 0.6708 (m-80) cc_final: 0.6452 (m-80) REVERT: L 73 ASP cc_start: 0.6558 (t0) cc_final: 0.5445 (m-30) REVERT: L 93 ILE cc_start: 0.6045 (mm) cc_final: 0.5811 (mm) REVERT: L 181 PHE cc_start: 0.4806 (m-10) cc_final: 0.4376 (m-80) REVERT: L 182 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6630 (mt-10) REVERT: L 223 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6278 (tpt90) REVERT: L 240 ASN cc_start: 0.5559 (t0) cc_final: 0.5329 (p0) REVERT: L 360 ASP cc_start: 0.6530 (m-30) cc_final: 0.6313 (m-30) REVERT: L 361 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6299 (mm-30) REVERT: L 386 TYR cc_start: 0.5644 (m-80) cc_final: 0.4932 (m-80) outliers start: 93 outliers final: 1 residues processed: 999 average time/residue: 0.8076 time to fit residues: 964.8471 Evaluate side-chains 706 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 692 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 223 ARG Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain I residue 421 LYS Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain J residue 223 ARG Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain K residue 223 ARG Chi-restraints excluded: chain L residue 223 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 0.0470 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 0.0980 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 34 ASN A 128 ASN A 281 HIS G 17 ASN G 24 GLN G 34 ASN G 128 ASN G 281 HIS H 17 ASN H 34 ASN H 281 HIS I 17 ASN I 34 ASN I 281 HIS B 17 ASN B 24 GLN B 34 ASN B 128 ASN B 281 HIS C 17 ASN C 34 ASN C 281 HIS J 17 ASN J 34 ASN J 128 ASN J 281 HIS D 24 GLN D 34 ASN D 128 ASN D 281 HIS E 17 ASN E 34 ASN E 128 ASN E 281 HIS F 17 ASN F 34 ASN F 128 ASN F 281 HIS K 17 ASN K 24 GLN K 34 ASN K 128 ASN K 281 HIS L 17 ASN L 34 ASN L 281 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.180961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.161770 restraints weight = 43563.509| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.47 r_work: 0.3865 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 42396 Z= 0.135 Angle : 0.584 8.088 57504 Z= 0.300 Chirality : 0.043 0.161 6300 Planarity : 0.004 0.039 7512 Dihedral : 4.830 59.137 5780 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.11 % Allowed : 10.37 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.11), residues: 5292 helix: 1.87 (0.11), residues: 2028 sheet: -0.32 (0.19), residues: 816 loop : -0.78 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 11 TYR 0.018 0.001 TYR I 285 PHE 0.015 0.001 PHE A 20 TRP 0.009 0.001 TRP H 435 HIS 0.004 0.001 HIS H 225 Details of bonding type rmsd covalent geometry : bond 0.00309 (42396) covalent geometry : angle 0.58392 (57504) hydrogen bonds : bond 0.04283 ( 1967) hydrogen bonds : angle 4.65229 ( 5721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 719 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6839 (mm-40) REVERT: A 73 ASP cc_start: 0.6818 (t0) cc_final: 0.6299 (m-30) REVERT: A 139 LYS cc_start: 0.8797 (mttt) cc_final: 0.8522 (mttm) REVERT: A 181 PHE cc_start: 0.5889 (m-10) cc_final: 0.5213 (m-80) REVERT: A 361 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7335 (mm-30) REVERT: A 398 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7465 (mm-30) REVERT: G 7 GLU cc_start: 0.6810 (mp0) cc_final: 0.6584 (mm-30) REVERT: G 16 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6721 (mm-40) REVERT: G 43 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7691 (mptt) REVERT: G 73 ASP cc_start: 0.6837 (t0) cc_final: 0.6463 (m-30) REVERT: G 181 PHE cc_start: 0.5949 (m-10) cc_final: 0.5309 (m-80) REVERT: G 223 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7638 (tpt170) REVERT: G 224 LYS cc_start: 0.8200 (pttt) cc_final: 0.7934 (pttm) REVERT: G 361 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7363 (mm-30) REVERT: H 16 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6791 (mm-40) REVERT: H 73 ASP cc_start: 0.6967 (t0) cc_final: 0.6635 (m-30) REVERT: H 144 ARG cc_start: 0.7230 (mmm160) cc_final: 0.6988 (mmm160) REVERT: H 181 PHE cc_start: 0.5832 (m-10) cc_final: 0.5271 (m-80) REVERT: H 223 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7563 (tpt90) REVERT: H 224 LYS cc_start: 0.8059 (pttt) cc_final: 0.7841 (pttm) REVERT: I 7 GLU cc_start: 0.6722 (mp0) cc_final: 0.6488 (mm-30) REVERT: I 73 ASP cc_start: 0.6861 (t0) cc_final: 0.6466 (m-30) REVERT: I 181 PHE cc_start: 0.6052 (m-10) cc_final: 0.5526 (m-80) REVERT: I 361 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7312 (mm-30) REVERT: I 398 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7401 (mm-30) REVERT: I 419 GLU cc_start: 0.7292 (tt0) cc_final: 0.6935 (mt-10) REVERT: I 443 ILE cc_start: 0.8461 (mp) cc_final: 0.8249 (mp) REVERT: B 7 GLU cc_start: 0.6909 (mp0) cc_final: 0.6665 (mm-30) REVERT: B 73 ASP cc_start: 0.6763 (t0) cc_final: 0.6492 (m-30) REVERT: B 181 PHE cc_start: 0.5911 (m-10) cc_final: 0.5382 (m-80) REVERT: B 223 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7644 (tpt170) REVERT: B 224 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7880 (pttm) REVERT: B 361 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7442 (mm-30) REVERT: C 43 LYS cc_start: 0.7879 (ttmm) cc_final: 0.7671 (mptt) REVERT: C 73 ASP cc_start: 0.7020 (t0) cc_final: 0.6767 (m-30) REVERT: C 114 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7786 (ttp-110) REVERT: C 181 PHE cc_start: 0.5856 (m-10) cc_final: 0.5269 (m-80) REVERT: C 223 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7600 (tpt90) REVERT: C 224 LYS cc_start: 0.8091 (pttt) cc_final: 0.7833 (pttm) REVERT: C 419 GLU cc_start: 0.7420 (tt0) cc_final: 0.7044 (mt-10) REVERT: J 7 GLU cc_start: 0.6809 (mp0) cc_final: 0.6579 (mm-30) REVERT: J 16 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6848 (mm-40) REVERT: J 43 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7383 (mptt) REVERT: J 67 ASP cc_start: 0.7032 (m-30) cc_final: 0.6795 (p0) REVERT: J 73 ASP cc_start: 0.6923 (t0) cc_final: 0.6458 (m-30) REVERT: J 181 PHE cc_start: 0.5926 (m-10) cc_final: 0.5255 (m-80) REVERT: J 361 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7347 (mm-30) REVERT: J 398 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7385 (mm-30) REVERT: D 73 ASP cc_start: 0.6874 (t0) cc_final: 0.6558 (m-30) REVERT: D 181 PHE cc_start: 0.5950 (m-10) cc_final: 0.5312 (m-80) REVERT: D 223 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7681 (tpt170) REVERT: D 224 LYS cc_start: 0.8158 (pttt) cc_final: 0.7902 (pttm) REVERT: D 361 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7317 (mm-30) REVERT: E 7 GLU cc_start: 0.6830 (mp0) cc_final: 0.6618 (mm-30) REVERT: E 16 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6807 (mm-40) REVERT: E 73 ASP cc_start: 0.7044 (t0) cc_final: 0.6641 (m-30) REVERT: E 144 ARG cc_start: 0.7292 (mmm160) cc_final: 0.6980 (mmm160) REVERT: E 181 PHE cc_start: 0.5847 (m-10) cc_final: 0.5220 (m-80) REVERT: E 248 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7714 (ptp) REVERT: F 16 GLN cc_start: 0.7722 (mt0) cc_final: 0.7275 (mm-40) REVERT: F 73 ASP cc_start: 0.6755 (t0) cc_final: 0.6330 (m-30) REVERT: F 181 PHE cc_start: 0.6147 (m-10) cc_final: 0.5623 (m-80) REVERT: F 223 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7531 (tpt90) REVERT: F 361 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7392 (mm-30) REVERT: F 398 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7404 (mm-30) REVERT: F 443 ILE cc_start: 0.8537 (mp) cc_final: 0.8322 (mp) REVERT: K 16 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6645 (mm-40) REVERT: K 73 ASP cc_start: 0.6855 (t0) cc_final: 0.6513 (m-30) REVERT: K 181 PHE cc_start: 0.5861 (m-10) cc_final: 0.5226 (m-80) REVERT: K 223 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7681 (tpt170) REVERT: K 224 LYS cc_start: 0.8209 (pttt) cc_final: 0.7947 (pttm) REVERT: K 361 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7313 (mm-30) REVERT: K 414 PHE cc_start: 0.8230 (t80) cc_final: 0.8022 (t80) REVERT: L 16 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6909 (mm-40) REVERT: L 43 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7475 (mptt) REVERT: L 73 ASP cc_start: 0.7042 (t0) cc_final: 0.6753 (m-30) REVERT: L 181 PHE cc_start: 0.5819 (m-10) cc_final: 0.5216 (m-80) REVERT: L 223 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7541 (tpt90) REVERT: L 224 LYS cc_start: 0.7994 (pttt) cc_final: 0.7785 (pttm) REVERT: L 398 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7519 (mm-30) outliers start: 133 outliers final: 52 residues processed: 783 average time/residue: 0.7634 time to fit residues: 723.3857 Evaluate side-chains 673 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 611 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 328 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 412 optimal weight: 0.0470 chunk 516 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 168 optimal weight: 0.0050 chunk 515 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 468 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 34 ASN G 17 ASN G 24 GLN G 34 ASN G 128 ASN H 17 ASN H 34 ASN I 17 ASN I 34 ASN I 128 ASN B 17 ASN B 24 GLN B 34 ASN B 128 ASN C 17 ASN C 34 ASN C 240 ASN J 34 ASN D 17 ASN D 34 ASN D 128 ASN E 17 ASN E 34 ASN E 240 ASN F 17 ASN F 34 ASN K 17 ASN K 34 ASN L 17 ASN L 34 ASN L 240 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.188018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166796 restraints weight = 44769.682| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.40 r_work: 0.3889 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 42396 Z= 0.106 Angle : 0.519 6.119 57504 Z= 0.268 Chirality : 0.041 0.150 6300 Planarity : 0.004 0.039 7512 Dihedral : 4.040 47.116 5728 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.21 % Allowed : 13.25 % Favored : 83.54 % 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: 0.60 (0.12), residues: 5292 helix: 2.02 (0.11), residues: 2028 sheet: -0.74 (0.18), residues: 900 loop : -0.53 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 114 TYR 0.015 0.001 TYR A 285 PHE 0.013 0.001 PHE C 414 TRP 0.007 0.001 TRP I 435 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00235 (42396) covalent geometry : angle 0.51876 (57504) hydrogen bonds : bond 0.03600 ( 1967) hydrogen bonds : angle 4.45384 ( 5721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 639 time to evaluate : 1.450 Fit side-chains REVERT: A 16 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6863 (mm-40) REVERT: A 73 ASP cc_start: 0.6575 (t0) cc_final: 0.6135 (m-30) REVERT: A 139 LYS cc_start: 0.8850 (mttt) cc_final: 0.8636 (mttm) REVERT: A 181 PHE cc_start: 0.5934 (m-10) cc_final: 0.5284 (m-80) REVERT: A 361 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7373 (mm-30) REVERT: A 398 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7496 (mm-30) REVERT: G 16 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6780 (mm-40) REVERT: G 17 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7495 (t0) REVERT: G 43 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7627 (mptt) REVERT: G 73 ASP cc_start: 0.6590 (t0) cc_final: 0.6323 (m-30) REVERT: G 181 PHE cc_start: 0.5937 (m-10) cc_final: 0.5288 (m-80) REVERT: G 223 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7705 (tpt170) REVERT: G 224 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7966 (pttm) REVERT: G 361 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7419 (mm-30) REVERT: H 16 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6901 (mm-40) REVERT: H 73 ASP cc_start: 0.6886 (t0) cc_final: 0.6632 (m-30) REVERT: H 144 ARG cc_start: 0.7266 (mmm160) cc_final: 0.7026 (mmm160) REVERT: H 181 PHE cc_start: 0.5878 (m-10) cc_final: 0.5306 (m-80) REVERT: H 223 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7553 (tpt90) REVERT: H 224 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7927 (pttm) REVERT: I 73 ASP cc_start: 0.6665 (t0) cc_final: 0.6390 (m-30) REVERT: I 181 PHE cc_start: 0.6064 (m-10) cc_final: 0.5538 (m-80) REVERT: I 223 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7724 (tpt90) REVERT: I 361 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7303 (mm-30) REVERT: I 386 TYR cc_start: 0.6933 (m-80) cc_final: 0.6608 (m-80) REVERT: I 398 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7422 (mm-30) REVERT: I 419 GLU cc_start: 0.7349 (tt0) cc_final: 0.7080 (mt-10) REVERT: B 17 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7609 (t0) REVERT: B 73 ASP cc_start: 0.6641 (t0) cc_final: 0.6399 (m-30) REVERT: B 181 PHE cc_start: 0.6021 (m-10) cc_final: 0.5498 (m-80) REVERT: B 223 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7570 (tpt170) REVERT: B 224 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7885 (pttm) REVERT: B 361 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7450 (mm-30) REVERT: C 101 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5659 (mpm) REVERT: C 114 ARG cc_start: 0.8036 (ttp-110) cc_final: 0.7804 (ttp-110) REVERT: C 181 PHE cc_start: 0.5956 (m-10) cc_final: 0.5309 (m-80) REVERT: C 224 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7923 (pttm) REVERT: C 398 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7704 (mm-30) REVERT: C 419 GLU cc_start: 0.7321 (tt0) cc_final: 0.7090 (mt-10) REVERT: J 16 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7021 (mm-40) REVERT: J 43 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7496 (mptt) REVERT: J 73 ASP cc_start: 0.6627 (t0) cc_final: 0.6249 (m-30) REVERT: J 181 PHE cc_start: 0.5996 (m-10) cc_final: 0.5330 (m-80) REVERT: J 223 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7751 (tpt90) REVERT: J 224 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7941 (pttm) REVERT: J 361 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7330 (mm-30) REVERT: J 398 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7522 (mm-30) REVERT: D 73 ASP cc_start: 0.6641 (t0) cc_final: 0.6437 (m-30) REVERT: D 181 PHE cc_start: 0.5992 (m-10) cc_final: 0.5362 (m-80) REVERT: D 223 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7701 (tpt170) REVERT: D 361 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7332 (mm-30) REVERT: E 16 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6953 (mm-40) REVERT: E 73 ASP cc_start: 0.6841 (t0) cc_final: 0.6567 (m-30) REVERT: E 181 PHE cc_start: 0.5841 (m-10) cc_final: 0.5207 (m-80) REVERT: F 16 GLN cc_start: 0.7730 (mt0) cc_final: 0.7513 (mm110) REVERT: F 73 ASP cc_start: 0.6561 (t0) cc_final: 0.6175 (m-30) REVERT: F 181 PHE cc_start: 0.6152 (m-10) cc_final: 0.5623 (m-80) REVERT: F 223 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7630 (tpt90) REVERT: F 224 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7793 (pttm) REVERT: F 338 ASP cc_start: 0.7810 (p0) cc_final: 0.7496 (p0) REVERT: F 361 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7338 (mm-30) REVERT: F 398 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7489 (mm-30) REVERT: K 16 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6760 (mm-40) REVERT: K 17 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7574 (t0) REVERT: K 73 ASP cc_start: 0.6632 (t0) cc_final: 0.6412 (m-30) REVERT: K 181 PHE cc_start: 0.5952 (m-10) cc_final: 0.5253 (m-80) REVERT: K 223 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7734 (tpt170) REVERT: K 224 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7979 (pttm) REVERT: K 361 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7415 (mm-30) REVERT: L 16 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6969 (mm-40) REVERT: L 43 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7611 (mptt) REVERT: L 73 ASP cc_start: 0.6944 (t0) cc_final: 0.6633 (m-30) REVERT: L 181 PHE cc_start: 0.5820 (m-10) cc_final: 0.5245 (m-80) REVERT: L 223 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7572 (tpt90) REVERT: L 398 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7588 (mm-30) outliers start: 137 outliers final: 31 residues processed: 706 average time/residue: 0.8071 time to fit residues: 688.5932 Evaluate side-chains 639 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 590 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 224 LYS Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 224 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 224 LYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 224 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 248 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 254 optimal weight: 4.9990 chunk 498 optimal weight: 0.0870 chunk 145 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 403 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 256 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 24 GLN G 34 ASN H 17 ASN H 34 ASN H 128 ASN I 17 ASN I 34 ASN B 24 GLN B 34 ASN C 17 ASN C 34 ASN J 34 ASN D 17 ASN D 24 GLN D 34 ASN E 17 ASN E 34 ASN E 128 ASN F 17 ASN F 24 GLN F 34 ASN K 24 GLN K 34 ASN K 128 ASN L 17 ASN L 34 ASN L 128 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.179100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158809 restraints weight = 43510.522| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.59 r_work: 0.3831 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42396 Z= 0.124 Angle : 0.531 6.145 57504 Z= 0.273 Chirality : 0.041 0.145 6300 Planarity : 0.004 0.039 7512 Dihedral : 4.087 43.038 5724 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.49 % Allowed : 13.62 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 5292 helix: 1.92 (0.11), residues: 2064 sheet: -0.81 (0.18), residues: 900 loop : -0.53 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 114 TYR 0.016 0.001 TYR F 285 PHE 0.020 0.001 PHE K 414 TRP 0.007 0.001 TRP L 77 HIS 0.003 0.001 HIS E 416 Details of bonding type rmsd covalent geometry : bond 0.00291 (42396) covalent geometry : angle 0.53082 (57504) hydrogen bonds : bond 0.03683 ( 1967) hydrogen bonds : angle 4.39068 ( 5721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 617 time to evaluate : 1.607 Fit side-chains REVERT: A 16 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6977 (mm-40) REVERT: A 73 ASP cc_start: 0.6754 (t0) cc_final: 0.6177 (m-30) REVERT: A 139 LYS cc_start: 0.8874 (mttt) cc_final: 0.8637 (mttm) REVERT: A 181 PHE cc_start: 0.5964 (m-10) cc_final: 0.5287 (m-80) REVERT: A 361 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7321 (mm-30) REVERT: A 398 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 419 GLU cc_start: 0.7374 (tt0) cc_final: 0.7078 (mt-10) REVERT: G 16 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6994 (mm-40) REVERT: G 17 ASN cc_start: 0.8071 (t0) cc_final: 0.7682 (t0) REVERT: G 43 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7581 (mptt) REVERT: G 73 ASP cc_start: 0.6778 (t0) cc_final: 0.6458 (m-30) REVERT: G 181 PHE cc_start: 0.6027 (m-10) cc_final: 0.5385 (m-80) REVERT: G 224 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7919 (pttm) REVERT: G 361 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7354 (mm-30) REVERT: H 16 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6970 (mm-40) REVERT: H 73 ASP cc_start: 0.7032 (t0) cc_final: 0.6521 (m-30) REVERT: H 144 ARG cc_start: 0.7249 (mmm160) cc_final: 0.6986 (mmm160) REVERT: H 181 PHE cc_start: 0.5922 (m-10) cc_final: 0.5344 (m-80) REVERT: H 223 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7554 (tpt90) REVERT: H 224 LYS cc_start: 0.8099 (pttt) cc_final: 0.7883 (pttm) REVERT: I 17 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7438 (t0) REVERT: I 73 ASP cc_start: 0.6810 (t0) cc_final: 0.6276 (m-30) REVERT: I 181 PHE cc_start: 0.6115 (m-10) cc_final: 0.5565 (m-80) REVERT: I 361 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7310 (mm-30) REVERT: I 398 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7502 (mm-30) REVERT: I 419 GLU cc_start: 0.7354 (tt0) cc_final: 0.7014 (mt-10) REVERT: B 17 ASN cc_start: 0.8118 (t0) cc_final: 0.7704 (t0) REVERT: B 51 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7557 (tpt) REVERT: B 73 ASP cc_start: 0.6879 (t0) cc_final: 0.6504 (m-30) REVERT: B 181 PHE cc_start: 0.6082 (m-10) cc_final: 0.5518 (m-80) REVERT: B 223 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7592 (tpt170) REVERT: B 224 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7744 (pttm) REVERT: B 361 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7403 (mm-30) REVERT: C 101 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.4572 (ttp) REVERT: C 181 PHE cc_start: 0.6104 (m-10) cc_final: 0.5414 (m-80) REVERT: C 224 LYS cc_start: 0.8093 (pttt) cc_final: 0.7877 (pttm) REVERT: C 398 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7731 (mm-30) REVERT: C 419 GLU cc_start: 0.7295 (tt0) cc_final: 0.7003 (mt-10) REVERT: J 16 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7028 (mm-40) REVERT: J 43 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7407 (mptt) REVERT: J 73 ASP cc_start: 0.6777 (t0) cc_final: 0.6177 (m-30) REVERT: J 93 ILE cc_start: 0.8308 (mm) cc_final: 0.8014 (mm) REVERT: J 139 LYS cc_start: 0.8926 (mttt) cc_final: 0.8705 (mttm) REVERT: J 181 PHE cc_start: 0.6014 (m-10) cc_final: 0.5372 (m-80) REVERT: J 210 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8690 (m) REVERT: J 361 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7289 (mm-30) REVERT: J 398 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7545 (mm-30) REVERT: D 17 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7511 (t0) REVERT: D 73 ASP cc_start: 0.6821 (t0) cc_final: 0.6508 (m-30) REVERT: D 181 PHE cc_start: 0.6043 (m-10) cc_final: 0.5377 (m-80) REVERT: D 265 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7535 (tt) REVERT: D 361 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7367 (mm-30) REVERT: E 16 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7017 (mm-40) REVERT: E 73 ASP cc_start: 0.7043 (t0) cc_final: 0.6546 (m-30) REVERT: E 181 PHE cc_start: 0.5915 (m-10) cc_final: 0.5297 (m-80) REVERT: F 17 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7468 (t0) REVERT: F 73 ASP cc_start: 0.6725 (t0) cc_final: 0.6164 (m-30) REVERT: F 181 PHE cc_start: 0.6228 (m-10) cc_final: 0.5639 (m-80) REVERT: F 223 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7822 (ttm-80) REVERT: F 338 ASP cc_start: 0.7893 (p0) cc_final: 0.7524 (p0) REVERT: F 361 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7330 (mm-30) REVERT: F 375 MET cc_start: 0.6116 (ptp) cc_final: 0.5740 (ptt) REVERT: F 398 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7475 (mm-30) REVERT: K 16 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6999 (mm-40) REVERT: K 17 ASN cc_start: 0.8085 (t0) cc_final: 0.7696 (t0) REVERT: K 73 ASP cc_start: 0.6887 (t0) cc_final: 0.6476 (m-30) REVERT: K 181 PHE cc_start: 0.5986 (m-10) cc_final: 0.5338 (m-80) REVERT: K 224 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7913 (pttm) REVERT: K 361 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7368 (mm-30) REVERT: L 16 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7018 (mm-40) REVERT: L 43 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7548 (mptt) REVERT: L 73 ASP cc_start: 0.7081 (t0) cc_final: 0.6567 (m-30) REVERT: L 181 PHE cc_start: 0.5879 (m-10) cc_final: 0.5226 (m-80) REVERT: L 398 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7676 (mm-30) outliers start: 149 outliers final: 64 residues processed: 689 average time/residue: 0.7981 time to fit residues: 666.1628 Evaluate side-chains 655 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 574 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 224 LYS Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 224 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 268 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 497 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 366 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 360 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 342 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 34 ASN ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN I 34 ASN B 34 ASN B 128 ASN C 34 ASN C 128 ASN J 34 ASN D 17 ASN D 24 GLN D 34 ASN D 128 ASN E 34 ASN F 34 ASN K 24 GLN K 34 ASN L 34 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.175988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156599 restraints weight = 43729.927| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.48 r_work: 0.3764 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 42396 Z= 0.146 Angle : 0.551 6.097 57504 Z= 0.284 Chirality : 0.043 0.156 6300 Planarity : 0.004 0.049 7512 Dihedral : 4.252 40.997 5724 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.03 % Allowed : 13.51 % Favored : 82.47 % 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: 0.42 (0.12), residues: 5292 helix: 1.82 (0.11), residues: 2064 sheet: -0.89 (0.18), residues: 900 loop : -0.60 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 109 TYR 0.015 0.001 TYR F 285 PHE 0.022 0.001 PHE D 414 TRP 0.007 0.001 TRP L 77 HIS 0.004 0.001 HIS H 416 Details of bonding type rmsd covalent geometry : bond 0.00352 (42396) covalent geometry : angle 0.55096 (57504) hydrogen bonds : bond 0.03940 ( 1967) hydrogen bonds : angle 4.42903 ( 5721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 604 time to evaluate : 1.623 Fit side-chains REVERT: A 16 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7052 (mm-40) REVERT: A 73 ASP cc_start: 0.6751 (t0) cc_final: 0.6197 (m-30) REVERT: A 139 LYS cc_start: 0.8883 (mttt) cc_final: 0.8637 (mttm) REVERT: A 181 PHE cc_start: 0.6050 (m-10) cc_final: 0.5395 (m-80) REVERT: A 210 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8741 (m) REVERT: A 338 ASP cc_start: 0.8006 (p0) cc_final: 0.7720 (p0) REVERT: A 398 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 419 GLU cc_start: 0.7410 (tt0) cc_final: 0.7115 (mt-10) REVERT: A 439 GLN cc_start: 0.7791 (tt0) cc_final: 0.7514 (mm-40) REVERT: G 16 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6966 (mm-40) REVERT: G 17 ASN cc_start: 0.8093 (t0) cc_final: 0.7809 (t0) REVERT: G 43 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7556 (mptt) REVERT: G 73 ASP cc_start: 0.6862 (t0) cc_final: 0.6497 (m-30) REVERT: G 181 PHE cc_start: 0.6185 (m-10) cc_final: 0.5516 (m-80) REVERT: G 224 LYS cc_start: 0.8148 (pttt) cc_final: 0.7910 (pttm) REVERT: G 361 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7387 (mm-30) REVERT: H 16 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7049 (mm-40) REVERT: H 67 ASP cc_start: 0.7239 (m-30) cc_final: 0.7004 (p0) REVERT: H 73 ASP cc_start: 0.7062 (t0) cc_final: 0.6554 (m-30) REVERT: H 144 ARG cc_start: 0.7321 (mmm160) cc_final: 0.7056 (mmm160) REVERT: H 181 PHE cc_start: 0.6072 (m-10) cc_final: 0.5492 (m-80) REVERT: I 17 ASN cc_start: 0.8043 (t0) cc_final: 0.7568 (t0) REVERT: I 73 ASP cc_start: 0.6925 (t0) cc_final: 0.6337 (m-30) REVERT: I 93 ILE cc_start: 0.8347 (mm) cc_final: 0.8078 (mm) REVERT: I 181 PHE cc_start: 0.6204 (m-10) cc_final: 0.5662 (m-80) REVERT: I 210 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8749 (m) REVERT: I 361 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7379 (mm-30) REVERT: I 398 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7513 (mm-30) REVERT: I 419 GLU cc_start: 0.7375 (tt0) cc_final: 0.7037 (mt-10) REVERT: B 17 ASN cc_start: 0.8059 (t0) cc_final: 0.7667 (t0) REVERT: B 73 ASP cc_start: 0.6941 (t0) cc_final: 0.6595 (m-30) REVERT: B 120 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: B 175 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6280 (tp30) REVERT: B 181 PHE cc_start: 0.6174 (m-10) cc_final: 0.5589 (m-80) REVERT: B 223 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7578 (tpt170) REVERT: B 224 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7736 (pttm) REVERT: B 361 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7390 (mm-30) REVERT: C 101 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.4539 (ttp) REVERT: C 181 PHE cc_start: 0.6258 (m-10) cc_final: 0.5581 (m-80) REVERT: C 224 LYS cc_start: 0.8042 (pttt) cc_final: 0.7832 (pttm) REVERT: C 398 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 419 GLU cc_start: 0.7322 (tt0) cc_final: 0.7064 (mt-10) REVERT: J 16 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7144 (mm-40) REVERT: J 43 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7428 (mptt) REVERT: J 73 ASP cc_start: 0.6832 (t0) cc_final: 0.6253 (m-30) REVERT: J 93 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8068 (mm) REVERT: J 139 LYS cc_start: 0.8947 (mttt) cc_final: 0.8727 (mttm) REVERT: J 181 PHE cc_start: 0.6080 (m-10) cc_final: 0.5376 (m-80) REVERT: J 361 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7310 (mm-30) REVERT: D 17 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7419 (t0) REVERT: D 73 ASP cc_start: 0.6868 (t0) cc_final: 0.6543 (m-30) REVERT: D 181 PHE cc_start: 0.6069 (m-10) cc_final: 0.5395 (m-10) REVERT: D 361 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7403 (mm-30) REVERT: D 398 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7525 (mm-30) REVERT: E 16 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7077 (mm-40) REVERT: E 73 ASP cc_start: 0.7040 (t0) cc_final: 0.6545 (m-30) REVERT: E 181 PHE cc_start: 0.6152 (m-10) cc_final: 0.5458 (m-80) REVERT: F 17 ASN cc_start: 0.8041 (t0) cc_final: 0.7585 (t0) REVERT: F 73 ASP cc_start: 0.6780 (t0) cc_final: 0.6192 (m-30) REVERT: F 181 PHE cc_start: 0.6295 (m-10) cc_final: 0.5710 (m-80) REVERT: F 210 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8732 (m) REVERT: F 338 ASP cc_start: 0.7965 (p0) cc_final: 0.7629 (p0) REVERT: F 361 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7385 (mm-30) REVERT: F 375 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5752 (ptt) REVERT: F 398 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7523 (mm-30) REVERT: K 16 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6990 (mm-40) REVERT: K 17 ASN cc_start: 0.8087 (t0) cc_final: 0.7806 (t0) REVERT: K 73 ASP cc_start: 0.6931 (t0) cc_final: 0.6493 (m-30) REVERT: K 181 PHE cc_start: 0.6115 (m-10) cc_final: 0.5487 (m-80) REVERT: K 224 LYS cc_start: 0.8135 (pttt) cc_final: 0.7887 (pttm) REVERT: K 361 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7353 (mm-30) REVERT: K 398 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7496 (mm-30) REVERT: L 16 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7086 (mm-40) REVERT: L 17 ASN cc_start: 0.7967 (t0) cc_final: 0.7434 (t0) REVERT: L 43 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7536 (mptt) REVERT: L 73 ASP cc_start: 0.7087 (t0) cc_final: 0.6572 (m-30) REVERT: L 181 PHE cc_start: 0.6081 (m-10) cc_final: 0.5478 (m-80) REVERT: L 398 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7779 (mm-30) outliers start: 172 outliers final: 72 residues processed: 703 average time/residue: 0.7610 time to fit residues: 652.9496 Evaluate side-chains 656 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 567 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 179 MET Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 383 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 405 optimal weight: 1.9990 chunk 461 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 307 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 493 optimal weight: 0.7980 chunk 359 optimal weight: 0.7980 chunk 498 optimal weight: 0.0060 chunk 44 optimal weight: 5.9990 chunk 467 optimal weight: 0.7980 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 34 ASN G 128 ASN H 34 ASN I 34 ASN I 128 ASN B 34 ASN C 34 ASN J 34 ASN D 17 ASN D 34 ASN E 34 ASN F 34 ASN K 34 ASN K 128 ASN L 34 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.184291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163081 restraints weight = 44966.203| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.40 r_work: 0.3853 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 42396 Z= 0.101 Angle : 0.505 6.084 57504 Z= 0.261 Chirality : 0.041 0.132 6300 Planarity : 0.004 0.044 7512 Dihedral : 4.072 36.999 5724 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.30 % Allowed : 14.47 % Favored : 82.23 % 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: 0.54 (0.12), residues: 5292 helix: 1.96 (0.11), residues: 2064 sheet: -0.85 (0.18), residues: 900 loop : -0.56 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 109 TYR 0.015 0.001 TYR I 285 PHE 0.027 0.001 PHE G 414 TRP 0.007 0.001 TRP L 77 HIS 0.002 0.000 HIS H 416 Details of bonding type rmsd covalent geometry : bond 0.00229 (42396) covalent geometry : angle 0.50536 (57504) hydrogen bonds : bond 0.03388 ( 1967) hydrogen bonds : angle 4.28744 ( 5721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 586 time to evaluate : 1.837 Fit side-chains REVERT: A 16 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7106 (mm-40) REVERT: A 73 ASP cc_start: 0.6710 (t0) cc_final: 0.6197 (m-30) REVERT: A 139 LYS cc_start: 0.8931 (mttt) cc_final: 0.8693 (mttm) REVERT: A 181 PHE cc_start: 0.5988 (m-10) cc_final: 0.5385 (m-80) REVERT: A 210 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8714 (m) REVERT: A 338 ASP cc_start: 0.7785 (p0) cc_final: 0.7404 (p0) REVERT: A 398 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7503 (mm-30) REVERT: G 16 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7041 (mm-40) REVERT: G 17 ASN cc_start: 0.8166 (t0) cc_final: 0.7855 (t0) REVERT: G 43 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7589 (mptt) REVERT: G 73 ASP cc_start: 0.6719 (t0) cc_final: 0.6451 (m-30) REVERT: G 181 PHE cc_start: 0.6085 (m-10) cc_final: 0.5477 (m-80) REVERT: G 224 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7913 (pttm) REVERT: G 361 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7331 (mm-30) REVERT: G 398 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7524 (mm-30) REVERT: H 73 ASP cc_start: 0.6940 (t0) cc_final: 0.6501 (m-30) REVERT: H 181 PHE cc_start: 0.6056 (m-10) cc_final: 0.5468 (m-80) REVERT: I 17 ASN cc_start: 0.8055 (t0) cc_final: 0.7610 (t0) REVERT: I 73 ASP cc_start: 0.6766 (t0) cc_final: 0.6248 (m-30) REVERT: I 101 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.4320 (ttm) REVERT: I 139 LYS cc_start: 0.8946 (mttt) cc_final: 0.8733 (mttm) REVERT: I 181 PHE cc_start: 0.6145 (m-10) cc_final: 0.5646 (m-80) REVERT: I 210 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8722 (m) REVERT: I 361 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7313 (mm-30) REVERT: I 419 GLU cc_start: 0.7396 (tt0) cc_final: 0.7087 (mt-10) REVERT: B 17 ASN cc_start: 0.8070 (t0) cc_final: 0.7725 (t0) REVERT: B 73 ASP cc_start: 0.6779 (t0) cc_final: 0.6515 (m-30) REVERT: B 120 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7200 (mm-30) REVERT: B 181 PHE cc_start: 0.6178 (m-10) cc_final: 0.5613 (m-80) REVERT: B 223 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7510 (tpt170) REVERT: B 224 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7796 (pttm) REVERT: B 361 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7357 (mm-30) REVERT: B 398 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7452 (mm-30) REVERT: C 101 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.4607 (ttp) REVERT: C 181 PHE cc_start: 0.6181 (m-10) cc_final: 0.5577 (m-80) REVERT: C 224 LYS cc_start: 0.8071 (pttt) cc_final: 0.7871 (pttm) REVERT: J 16 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7162 (mm-40) REVERT: J 43 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7470 (mptt) REVERT: J 73 ASP cc_start: 0.6656 (t0) cc_final: 0.6148 (m-30) REVERT: J 93 ILE cc_start: 0.8301 (mm) cc_final: 0.7977 (mm) REVERT: J 139 LYS cc_start: 0.8940 (mttt) cc_final: 0.8731 (mttm) REVERT: J 181 PHE cc_start: 0.5984 (m-10) cc_final: 0.5377 (m-80) REVERT: J 210 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8698 (m) REVERT: J 361 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7357 (mm-30) REVERT: D 73 ASP cc_start: 0.6791 (t0) cc_final: 0.6518 (m-30) REVERT: D 181 PHE cc_start: 0.6081 (m-10) cc_final: 0.5435 (m-10) REVERT: D 361 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7340 (mm-30) REVERT: D 414 PHE cc_start: 0.8168 (t80) cc_final: 0.7925 (t80) REVERT: E 73 ASP cc_start: 0.6965 (t0) cc_final: 0.6529 (m-30) REVERT: E 181 PHE cc_start: 0.6113 (m-10) cc_final: 0.5462 (m-80) REVERT: F 17 ASN cc_start: 0.8004 (t0) cc_final: 0.7577 (t0) REVERT: F 73 ASP cc_start: 0.6630 (t0) cc_final: 0.6127 (m-30) REVERT: F 139 LYS cc_start: 0.8945 (mttt) cc_final: 0.8742 (mttm) REVERT: F 181 PHE cc_start: 0.6204 (m-10) cc_final: 0.5693 (m-80) REVERT: F 210 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8729 (m) REVERT: F 361 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7339 (mm-30) REVERT: F 375 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.5822 (ptt) REVERT: F 398 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7516 (mm-30) REVERT: K 17 ASN cc_start: 0.8157 (t0) cc_final: 0.7853 (t0) REVERT: K 73 ASP cc_start: 0.6826 (t0) cc_final: 0.6486 (m-30) REVERT: K 181 PHE cc_start: 0.6136 (m-10) cc_final: 0.5549 (m-10) REVERT: K 224 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7915 (pttm) REVERT: K 361 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7322 (mm-30) REVERT: K 398 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7554 (mm-30) REVERT: L 16 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7114 (mm-40) REVERT: L 43 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7555 (mptt) REVERT: L 73 ASP cc_start: 0.6972 (t0) cc_final: 0.6529 (m-30) REVERT: L 117 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7272 (ttmm) REVERT: L 181 PHE cc_start: 0.6088 (m-10) cc_final: 0.5587 (m-80) REVERT: L 398 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7684 (mm-30) outliers start: 141 outliers final: 60 residues processed: 667 average time/residue: 0.7676 time to fit residues: 624.7004 Evaluate side-chains 631 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 555 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 224 LYS Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 224 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 383 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 209 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 421 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 467 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 306 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 372 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 302 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 34 ASN H 34 ASN I 34 ASN B 34 ASN C 34 ASN C 128 ASN J 34 ASN D 17 ASN D 34 ASN E 34 ASN F 34 ASN K 34 ASN L 34 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.183089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161776 restraints weight = 44786.919| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.41 r_work: 0.3838 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42396 Z= 0.112 Angle : 0.517 6.086 57504 Z= 0.266 Chirality : 0.041 0.135 6300 Planarity : 0.004 0.037 7512 Dihedral : 4.094 34.492 5724 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.11 % Allowed : 14.63 % Favored : 82.26 % 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: 0.52 (0.12), residues: 5292 helix: 1.94 (0.11), residues: 2064 sheet: -0.85 (0.18), residues: 900 loop : -0.58 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 283 TYR 0.015 0.001 TYR I 285 PHE 0.010 0.001 PHE J 251 TRP 0.007 0.001 TRP L 77 HIS 0.003 0.001 HIS H 416 Details of bonding type rmsd covalent geometry : bond 0.00264 (42396) covalent geometry : angle 0.51701 (57504) hydrogen bonds : bond 0.03488 ( 1967) hydrogen bonds : angle 4.28441 ( 5721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 568 time to evaluate : 1.585 Fit side-chains REVERT: A 16 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7188 (mm-40) REVERT: A 73 ASP cc_start: 0.6627 (t0) cc_final: 0.6149 (m-30) REVERT: A 139 LYS cc_start: 0.8928 (mttt) cc_final: 0.8725 (mttm) REVERT: A 181 PHE cc_start: 0.6010 (m-10) cc_final: 0.5427 (m-80) REVERT: A 210 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8723 (m) REVERT: A 398 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7522 (mm-30) REVERT: G 17 ASN cc_start: 0.8232 (t0) cc_final: 0.7890 (t0) REVERT: G 43 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7653 (mptt) REVERT: G 73 ASP cc_start: 0.6743 (t0) cc_final: 0.6489 (m-30) REVERT: G 181 PHE cc_start: 0.6156 (m-10) cc_final: 0.5569 (m-80) REVERT: G 224 LYS cc_start: 0.8209 (pttt) cc_final: 0.7980 (pttm) REVERT: G 361 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7322 (mm-30) REVERT: G 398 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7488 (mm-30) REVERT: H 73 ASP cc_start: 0.6944 (t0) cc_final: 0.6488 (m-30) REVERT: H 181 PHE cc_start: 0.6066 (m-10) cc_final: 0.5491 (m-80) REVERT: I 17 ASN cc_start: 0.8175 (t0) cc_final: 0.7731 (t0) REVERT: I 73 ASP cc_start: 0.6751 (t0) cc_final: 0.6302 (m-30) REVERT: I 93 ILE cc_start: 0.8314 (mm) cc_final: 0.8054 (mm) REVERT: I 101 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.4390 (ttm) REVERT: I 139 LYS cc_start: 0.8962 (mttt) cc_final: 0.8750 (mttm) REVERT: I 181 PHE cc_start: 0.6146 (m-10) cc_final: 0.5651 (m-80) REVERT: I 210 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8753 (m) REVERT: I 361 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7330 (mm-30) REVERT: I 398 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7524 (mm-30) REVERT: I 419 GLU cc_start: 0.7499 (tt0) cc_final: 0.7210 (mt-10) REVERT: B 17 ASN cc_start: 0.8128 (t0) cc_final: 0.7818 (t0) REVERT: B 73 ASP cc_start: 0.6762 (t0) cc_final: 0.6520 (m-30) REVERT: B 120 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: B 175 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6285 (tp30) REVERT: B 181 PHE cc_start: 0.6174 (m-10) cc_final: 0.5595 (m-80) REVERT: B 223 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7577 (tpt170) REVERT: B 224 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7779 (pttm) REVERT: B 361 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7343 (mm-30) REVERT: B 398 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7507 (mm-30) REVERT: C 101 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.4627 (ttp) REVERT: C 181 PHE cc_start: 0.6169 (m-10) cc_final: 0.5560 (m-80) REVERT: J 16 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7214 (mm-40) REVERT: J 43 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7477 (mptt) REVERT: J 73 ASP cc_start: 0.6654 (t0) cc_final: 0.6195 (m-30) REVERT: J 93 ILE cc_start: 0.8339 (mm) cc_final: 0.8078 (mm) REVERT: J 139 LYS cc_start: 0.8953 (mttt) cc_final: 0.8744 (mttm) REVERT: J 181 PHE cc_start: 0.6010 (m-10) cc_final: 0.5414 (m-80) REVERT: J 361 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7397 (mm-30) REVERT: D 73 ASP cc_start: 0.6804 (t0) cc_final: 0.6543 (m-30) REVERT: D 121 GLU cc_start: 0.6597 (pp20) cc_final: 0.6284 (pt0) REVERT: D 181 PHE cc_start: 0.6084 (m-10) cc_final: 0.5451 (m-80) REVERT: D 361 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7331 (mm-30) REVERT: D 375 MET cc_start: 0.5455 (ptp) cc_final: 0.5201 (ptt) REVERT: D 398 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7501 (mm-30) REVERT: E 73 ASP cc_start: 0.6961 (t0) cc_final: 0.6533 (m-30) REVERT: E 181 PHE cc_start: 0.6170 (m-10) cc_final: 0.5602 (m-80) REVERT: F 17 ASN cc_start: 0.8158 (t0) cc_final: 0.7817 (t0) REVERT: F 73 ASP cc_start: 0.6632 (t0) cc_final: 0.6179 (m-30) REVERT: F 181 PHE cc_start: 0.6272 (m-10) cc_final: 0.5747 (m-80) REVERT: F 210 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8730 (m) REVERT: F 361 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7368 (mm-30) REVERT: F 375 MET cc_start: 0.6092 (OUTLIER) cc_final: 0.5891 (ptt) REVERT: K 17 ASN cc_start: 0.8231 (t0) cc_final: 0.7923 (t0) REVERT: K 73 ASP cc_start: 0.6750 (t0) cc_final: 0.6505 (m-30) REVERT: K 181 PHE cc_start: 0.6193 (m-10) cc_final: 0.5609 (m-10) REVERT: K 224 LYS cc_start: 0.8187 (pttt) cc_final: 0.7946 (pttm) REVERT: K 265 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7519 (tt) REVERT: K 361 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7344 (mm-30) REVERT: K 398 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7501 (mm-30) REVERT: L 16 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7163 (mm-40) REVERT: L 43 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7591 (mptt) REVERT: L 73 ASP cc_start: 0.6937 (t0) cc_final: 0.6518 (m-30) REVERT: L 117 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7358 (ttmm) REVERT: L 181 PHE cc_start: 0.6086 (m-10) cc_final: 0.5606 (m-80) outliers start: 133 outliers final: 70 residues processed: 647 average time/residue: 0.7642 time to fit residues: 603.4125 Evaluate side-chains 634 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 550 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 101 MET Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 51 MET Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 383 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 219 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 389 optimal weight: 10.0000 chunk 402 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 395 optimal weight: 3.9990 chunk 424 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 34 ASN H 34 ASN I 34 ASN B 34 ASN C 34 ASN J 34 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 34 ASN F 34 ASN K 34 ASN L 34 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.171985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151689 restraints weight = 44081.720| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.60 r_work: 0.3674 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 42396 Z= 0.187 Angle : 0.600 6.277 57504 Z= 0.309 Chirality : 0.045 0.168 6300 Planarity : 0.004 0.043 7512 Dihedral : 4.508 37.364 5724 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.79 % Allowed : 14.93 % Favored : 82.28 % 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: 0.21 (0.12), residues: 5292 helix: 1.68 (0.11), residues: 2064 sheet: -1.01 (0.17), residues: 924 loop : -0.75 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 283 TYR 0.016 0.002 TYR A 285 PHE 0.046 0.002 PHE B 414 TRP 0.006 0.002 TRP C 435 HIS 0.005 0.001 HIS C 416 Details of bonding type rmsd covalent geometry : bond 0.00464 (42396) covalent geometry : angle 0.60044 (57504) hydrogen bonds : bond 0.04352 ( 1967) hydrogen bonds : angle 4.51632 ( 5721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 587 time to evaluate : 1.600 Fit side-chains REVERT: A 16 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7256 (mm-40) REVERT: A 73 ASP cc_start: 0.6808 (t0) cc_final: 0.6339 (m-30) REVERT: A 139 LYS cc_start: 0.8975 (mttt) cc_final: 0.8728 (mttm) REVERT: A 181 PHE cc_start: 0.6112 (m-10) cc_final: 0.5458 (m-80) REVERT: A 210 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8650 (m) REVERT: A 338 ASP cc_start: 0.8140 (p0) cc_final: 0.7833 (p0) REVERT: A 398 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 419 GLU cc_start: 0.7519 (tt0) cc_final: 0.7163 (mt-10) REVERT: G 17 ASN cc_start: 0.8281 (t0) cc_final: 0.7977 (t0) REVERT: G 43 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7602 (mptt) REVERT: G 73 ASP cc_start: 0.7008 (t0) cc_final: 0.6639 (m-30) REVERT: G 181 PHE cc_start: 0.6209 (m-10) cc_final: 0.5512 (m-10) REVERT: G 224 LYS cc_start: 0.8180 (pttt) cc_final: 0.7955 (pttm) REVERT: G 361 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7362 (mm-30) REVERT: G 398 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7523 (mm-30) REVERT: H 73 ASP cc_start: 0.7141 (t0) cc_final: 0.6587 (m-30) REVERT: H 145 ARG cc_start: 0.7082 (mmm160) cc_final: 0.5286 (ptm-80) REVERT: H 181 PHE cc_start: 0.6173 (m-10) cc_final: 0.5554 (m-10) REVERT: I 17 ASN cc_start: 0.8153 (t0) cc_final: 0.7792 (t0) REVERT: I 73 ASP cc_start: 0.6890 (t0) cc_final: 0.6403 (m-30) REVERT: I 139 LYS cc_start: 0.9004 (mttt) cc_final: 0.8781 (mttm) REVERT: I 178 GLU cc_start: 0.7711 (tt0) cc_final: 0.7463 (tt0) REVERT: I 181 PHE cc_start: 0.6265 (m-10) cc_final: 0.5727 (m-80) REVERT: I 210 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8698 (m) REVERT: I 338 ASP cc_start: 0.8020 (p0) cc_final: 0.7686 (p0) REVERT: I 361 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7443 (mm-30) REVERT: I 419 GLU cc_start: 0.7518 (tt0) cc_final: 0.7164 (mt-10) REVERT: B 17 ASN cc_start: 0.8223 (t0) cc_final: 0.7899 (t0) REVERT: B 73 ASP cc_start: 0.6950 (t0) cc_final: 0.6593 (m-30) REVERT: B 120 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: B 175 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6409 (tp30) REVERT: B 181 PHE cc_start: 0.6263 (m-10) cc_final: 0.5631 (m-10) REVERT: B 223 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7680 (tpt170) REVERT: B 224 LYS cc_start: 0.8112 (pttt) cc_final: 0.7828 (pttm) REVERT: B 361 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7389 (mm-30) REVERT: B 398 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7535 (mm-30) REVERT: C 181 PHE cc_start: 0.6354 (m-10) cc_final: 0.5810 (m-80) REVERT: C 419 GLU cc_start: 0.7520 (tt0) cc_final: 0.7252 (mt-10) REVERT: C 443 ILE cc_start: 0.8348 (mp) cc_final: 0.8138 (mp) REVERT: J 16 GLN cc_start: 0.7707 (mt0) cc_final: 0.7251 (mt0) REVERT: J 43 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7382 (mptt) REVERT: J 73 ASP cc_start: 0.6980 (t0) cc_final: 0.6429 (m-30) REVERT: J 93 ILE cc_start: 0.8419 (mm) cc_final: 0.8190 (mm) REVERT: J 139 LYS cc_start: 0.8995 (mttt) cc_final: 0.8771 (mttm) REVERT: J 181 PHE cc_start: 0.6140 (m-10) cc_final: 0.5465 (m-80) REVERT: J 360 ASP cc_start: 0.7196 (m-30) cc_final: 0.6892 (m-30) REVERT: J 361 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7403 (mm-30) REVERT: D 73 ASP cc_start: 0.7015 (t0) cc_final: 0.6646 (m-30) REVERT: D 121 GLU cc_start: 0.6768 (pp20) cc_final: 0.6512 (pt0) REVERT: D 145 ARG cc_start: 0.7277 (mmm160) cc_final: 0.5480 (ptm-80) REVERT: D 181 PHE cc_start: 0.6168 (m-10) cc_final: 0.5489 (m-10) REVERT: D 361 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7359 (mm-30) REVERT: D 398 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7590 (mm-30) REVERT: E 73 ASP cc_start: 0.7126 (t0) cc_final: 0.6566 (m-30) REVERT: E 145 ARG cc_start: 0.7102 (mmm160) cc_final: 0.5296 (ptm-80) REVERT: E 181 PHE cc_start: 0.6329 (m-10) cc_final: 0.5662 (m-10) REVERT: E 398 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7655 (mm-30) REVERT: F 17 ASN cc_start: 0.8126 (t0) cc_final: 0.7776 (t0) REVERT: F 73 ASP cc_start: 0.6851 (t0) cc_final: 0.6363 (m-30) REVERT: F 181 PHE cc_start: 0.6314 (m-10) cc_final: 0.5746 (m-80) REVERT: F 210 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8637 (m) REVERT: F 338 ASP cc_start: 0.8067 (p0) cc_final: 0.7761 (p0) REVERT: F 361 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7389 (mm-30) REVERT: F 375 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5767 (ptt) REVERT: F 398 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7580 (mm-30) REVERT: K 17 ASN cc_start: 0.8338 (t0) cc_final: 0.8009 (t0) REVERT: K 73 ASP cc_start: 0.7056 (t0) cc_final: 0.6675 (m-30) REVERT: K 145 ARG cc_start: 0.7240 (mmm160) cc_final: 0.5542 (ptm-80) REVERT: K 181 PHE cc_start: 0.6212 (m-10) cc_final: 0.5514 (m-10) REVERT: K 224 LYS cc_start: 0.8154 (pttt) cc_final: 0.7926 (pttm) REVERT: K 361 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7445 (mm-30) REVERT: K 375 MET cc_start: 0.5651 (ptp) cc_final: 0.5444 (ptp) REVERT: K 398 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7560 (mm-30) REVERT: L 16 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7185 (mm110) REVERT: L 17 ASN cc_start: 0.8094 (t0) cc_final: 0.7412 (t0) REVERT: L 43 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7493 (mptt) REVERT: L 73 ASP cc_start: 0.7157 (t0) cc_final: 0.6584 (m-30) REVERT: L 181 PHE cc_start: 0.6227 (m-10) cc_final: 0.5573 (m-10) outliers start: 119 outliers final: 55 residues processed: 671 average time/residue: 0.7399 time to fit residues: 606.1158 Evaluate side-chains 616 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 553 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain G residue 34 ASN Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 383 THR Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 383 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 404 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 158 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 517 optimal weight: 0.0770 chunk 483 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 206 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 34 ASN H 34 ASN I 34 ASN B 34 ASN C 34 ASN J 34 ASN J 128 ASN D 34 ASN E 34 ASN F 34 ASN K 34 ASN L 34 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.177727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158677 restraints weight = 43579.656| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.47 r_work: 0.3827 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42396 Z= 0.102 Angle : 0.523 6.124 57504 Z= 0.271 Chirality : 0.041 0.156 6300 Planarity : 0.004 0.038 7512 Dihedral : 4.174 32.183 5724 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.08 % Allowed : 15.73 % Favored : 82.19 % 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: 0.42 (0.12), residues: 5292 helix: 1.93 (0.11), residues: 2064 sheet: -0.91 (0.19), residues: 768 loop : -0.74 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 283 TYR 0.016 0.001 TYR I 285 PHE 0.017 0.001 PHE A 414 TRP 0.006 0.001 TRP C 435 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00227 (42396) covalent geometry : angle 0.52251 (57504) hydrogen bonds : bond 0.03370 ( 1967) hydrogen bonds : angle 4.34512 ( 5721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 581 time to evaluate : 1.710 Fit side-chains REVERT: A 16 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7224 (mm-40) REVERT: A 73 ASP cc_start: 0.6724 (t0) cc_final: 0.6170 (m-30) REVERT: A 139 LYS cc_start: 0.8919 (mttt) cc_final: 0.8545 (mttm) REVERT: A 181 PHE cc_start: 0.5966 (m-10) cc_final: 0.5400 (m-80) REVERT: A 338 ASP cc_start: 0.7957 (p0) cc_final: 0.7543 (p0) REVERT: A 398 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7353 (mm-30) REVERT: G 17 ASN cc_start: 0.8226 (t0) cc_final: 0.7887 (t0) REVERT: G 43 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7569 (mptt) REVERT: G 73 ASP cc_start: 0.6832 (t0) cc_final: 0.6516 (m-30) REVERT: G 121 GLU cc_start: 0.6465 (pp20) cc_final: 0.6191 (pt0) REVERT: G 181 PHE cc_start: 0.6176 (m-10) cc_final: 0.5580 (m-10) REVERT: G 224 LYS cc_start: 0.8107 (pttt) cc_final: 0.7875 (pttm) REVERT: G 361 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7256 (mm-30) REVERT: G 398 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7429 (mm-30) REVERT: H 73 ASP cc_start: 0.7031 (t0) cc_final: 0.6520 (m-30) REVERT: H 145 ARG cc_start: 0.7096 (mmm160) cc_final: 0.5441 (ptm-80) REVERT: H 181 PHE cc_start: 0.6156 (m-10) cc_final: 0.5611 (m-10) REVERT: I 17 ASN cc_start: 0.8093 (t0) cc_final: 0.7699 (t0) REVERT: I 73 ASP cc_start: 0.6721 (t0) cc_final: 0.6190 (m-30) REVERT: I 139 LYS cc_start: 0.8976 (mttt) cc_final: 0.8608 (mttm) REVERT: I 181 PHE cc_start: 0.6202 (m-10) cc_final: 0.5704 (m-80) REVERT: I 210 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8662 (m) REVERT: I 361 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7342 (mm-30) REVERT: I 398 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7352 (mm-30) REVERT: I 419 GLU cc_start: 0.7370 (tt0) cc_final: 0.7024 (mt-10) REVERT: B 17 ASN cc_start: 0.8113 (t0) cc_final: 0.7799 (t0) REVERT: B 73 ASP cc_start: 0.6800 (t0) cc_final: 0.6354 (m-30) REVERT: B 181 PHE cc_start: 0.6269 (m-10) cc_final: 0.5716 (m-10) REVERT: B 224 LYS cc_start: 0.8010 (pttt) cc_final: 0.7710 (pttm) REVERT: B 361 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7294 (mm-30) REVERT: B 398 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7500 (mm-30) REVERT: C 181 PHE cc_start: 0.6316 (m-10) cc_final: 0.5728 (m-10) REVERT: C 443 ILE cc_start: 0.8483 (mp) cc_final: 0.8269 (mp) REVERT: J 16 GLN cc_start: 0.7652 (mt0) cc_final: 0.7270 (mm110) REVERT: J 43 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7365 (mptt) REVERT: J 73 ASP cc_start: 0.6664 (t0) cc_final: 0.6174 (m-30) REVERT: J 93 ILE cc_start: 0.8312 (mm) cc_final: 0.8044 (mm) REVERT: J 139 LYS cc_start: 0.8962 (mttt) cc_final: 0.8733 (mttm) REVERT: J 181 PHE cc_start: 0.6012 (m-10) cc_final: 0.5420 (m-80) REVERT: J 361 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7317 (mm-30) REVERT: J 398 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7364 (mm-30) REVERT: D 73 ASP cc_start: 0.6819 (t0) cc_final: 0.6473 (m-30) REVERT: D 121 GLU cc_start: 0.6590 (pp20) cc_final: 0.6338 (pt0) REVERT: D 181 PHE cc_start: 0.6134 (m-10) cc_final: 0.5505 (m-10) REVERT: D 361 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7310 (mm-30) REVERT: D 398 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7473 (mm-30) REVERT: D 414 PHE cc_start: 0.8102 (t80) cc_final: 0.7886 (t80) REVERT: E 73 ASP cc_start: 0.7031 (t0) cc_final: 0.6490 (m-30) REVERT: E 145 ARG cc_start: 0.7113 (mmm160) cc_final: 0.5473 (ptm-80) REVERT: E 181 PHE cc_start: 0.6207 (m-10) cc_final: 0.5624 (m-10) REVERT: F 17 ASN cc_start: 0.8031 (t0) cc_final: 0.7639 (t0) REVERT: F 73 ASP cc_start: 0.6725 (t0) cc_final: 0.6172 (m-30) REVERT: F 181 PHE cc_start: 0.6188 (m-10) cc_final: 0.5658 (m-80) REVERT: F 210 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8638 (m) REVERT: F 361 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7289 (mm-30) REVERT: F 398 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7517 (mm-30) REVERT: K 17 ASN cc_start: 0.8226 (t0) cc_final: 0.7903 (t0) REVERT: K 73 ASP cc_start: 0.6852 (t0) cc_final: 0.6524 (m-30) REVERT: K 181 PHE cc_start: 0.6184 (m-10) cc_final: 0.5620 (m-10) REVERT: K 224 LYS cc_start: 0.8069 (pttt) cc_final: 0.7825 (pttm) REVERT: K 361 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7312 (mm-30) REVERT: K 375 MET cc_start: 0.5559 (ptp) cc_final: 0.5341 (ptt) REVERT: K 398 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7494 (mm-30) REVERT: L 16 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7147 (mm-40) REVERT: L 17 ASN cc_start: 0.8009 (t0) cc_final: 0.7372 (t0) REVERT: L 43 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7474 (mptt) REVERT: L 73 ASP cc_start: 0.7016 (t0) cc_final: 0.6485 (m-30) REVERT: L 181 PHE cc_start: 0.6119 (m-10) cc_final: 0.5619 (m-80) outliers start: 89 outliers final: 40 residues processed: 645 average time/residue: 0.7904 time to fit residues: 619.3760 Evaluate side-chains 588 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 544 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain L residue 383 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 290 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 448 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 464 optimal weight: 6.9990 chunk 230 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 465 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 24 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN B 34 ASN C 34 ASN C 128 ASN J 34 ASN J 128 ASN D 24 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN E 34 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN K 34 ASN ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.182855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.161860 restraints weight = 44778.322| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.40 r_work: 0.3838 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 42396 Z= 0.134 Angle : 0.616 59.200 57504 Z= 0.335 Chirality : 0.042 0.472 6300 Planarity : 0.004 0.038 7512 Dihedral : 4.180 32.197 5724 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.50 % Allowed : 16.90 % Favored : 81.60 % Cbeta Deviations : 0.02 % 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: 0.43 (0.12), residues: 5292 helix: 1.95 (0.11), residues: 2064 sheet: -0.91 (0.19), residues: 768 loop : -0.74 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 283 TYR 0.015 0.001 TYR I 285 PHE 0.016 0.001 PHE G 414 TRP 0.008 0.001 TRP C 77 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00301 (42396) covalent geometry : angle 0.61602 (57504) hydrogen bonds : bond 0.03398 ( 1967) hydrogen bonds : angle 4.34397 ( 5721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 549 time to evaluate : 2.496 Fit side-chains REVERT: A 16 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7266 (mm-40) REVERT: A 73 ASP cc_start: 0.6662 (t0) cc_final: 0.6222 (m-30) REVERT: A 139 LYS cc_start: 0.8903 (mttt) cc_final: 0.8555 (mttm) REVERT: A 181 PHE cc_start: 0.6011 (m-10) cc_final: 0.5429 (m-80) REVERT: A 338 ASP cc_start: 0.7906 (p0) cc_final: 0.7503 (p0) REVERT: A 398 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7396 (mm-30) REVERT: G 17 ASN cc_start: 0.8258 (t0) cc_final: 0.7934 (t0) REVERT: G 43 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7641 (mptt) REVERT: G 73 ASP cc_start: 0.6772 (t0) cc_final: 0.6531 (m-30) REVERT: G 121 GLU cc_start: 0.6467 (pp20) cc_final: 0.6173 (pt0) REVERT: G 181 PHE cc_start: 0.6159 (m-10) cc_final: 0.5573 (m-10) REVERT: G 224 LYS cc_start: 0.8153 (pttt) cc_final: 0.7922 (pttm) REVERT: G 398 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7468 (mm-30) REVERT: H 34 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8335 (t0) REVERT: H 73 ASP cc_start: 0.6971 (t0) cc_final: 0.6558 (m-30) REVERT: H 145 ARG cc_start: 0.7143 (mmm160) cc_final: 0.5585 (ptm-80) REVERT: H 181 PHE cc_start: 0.6161 (m-10) cc_final: 0.5615 (m-10) REVERT: I 17 ASN cc_start: 0.8130 (t0) cc_final: 0.7761 (t0) REVERT: I 73 ASP cc_start: 0.6662 (t0) cc_final: 0.6224 (m-30) REVERT: I 139 LYS cc_start: 0.8974 (mttt) cc_final: 0.8630 (mttm) REVERT: I 181 PHE cc_start: 0.6201 (m-10) cc_final: 0.5697 (m-80) REVERT: I 210 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8697 (m) REVERT: I 361 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7386 (mm-30) REVERT: I 398 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7400 (mm-30) REVERT: I 419 GLU cc_start: 0.7419 (tt0) cc_final: 0.7121 (mt-10) REVERT: B 17 ASN cc_start: 0.8139 (t0) cc_final: 0.7831 (t0) REVERT: B 73 ASP cc_start: 0.6718 (t0) cc_final: 0.6368 (m-30) REVERT: B 181 PHE cc_start: 0.6271 (m-10) cc_final: 0.5720 (m-10) REVERT: B 223 ARG cc_start: 0.8157 (tpp-160) cc_final: 0.7671 (tpt170) REVERT: B 224 LYS cc_start: 0.8055 (pttt) cc_final: 0.7765 (pttm) REVERT: B 361 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7310 (mm-30) REVERT: B 398 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 181 PHE cc_start: 0.6327 (m-10) cc_final: 0.5851 (m-80) REVERT: J 16 GLN cc_start: 0.7631 (mt0) cc_final: 0.7319 (mm110) REVERT: J 43 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7477 (mptt) REVERT: J 73 ASP cc_start: 0.6607 (t0) cc_final: 0.6151 (m-30) REVERT: J 93 ILE cc_start: 0.8340 (mm) cc_final: 0.8099 (mm) REVERT: J 181 PHE cc_start: 0.6023 (m-10) cc_final: 0.5428 (m-80) REVERT: J 361 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7355 (mm-30) REVERT: J 398 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 73 ASP cc_start: 0.6752 (t0) cc_final: 0.6475 (m-30) REVERT: D 121 GLU cc_start: 0.6608 (pp20) cc_final: 0.6333 (pt0) REVERT: D 181 PHE cc_start: 0.6121 (m-10) cc_final: 0.5503 (m-10) REVERT: D 361 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7346 (mm-30) REVERT: D 398 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7500 (mm-30) REVERT: E 73 ASP cc_start: 0.7004 (t0) cc_final: 0.6537 (m-30) REVERT: E 145 ARG cc_start: 0.7150 (mmm160) cc_final: 0.5606 (ptm-80) REVERT: E 181 PHE cc_start: 0.6212 (m-10) cc_final: 0.5688 (m-80) REVERT: F 17 ASN cc_start: 0.8073 (t0) cc_final: 0.7685 (t0) REVERT: F 73 ASP cc_start: 0.6667 (t0) cc_final: 0.6208 (m-30) REVERT: F 181 PHE cc_start: 0.6203 (m-10) cc_final: 0.5685 (m-80) REVERT: F 210 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8666 (m) REVERT: F 361 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7336 (mm-30) REVERT: F 398 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7557 (mm-30) REVERT: K 17 ASN cc_start: 0.8247 (t0) cc_final: 0.7932 (t0) REVERT: K 73 ASP cc_start: 0.6772 (t0) cc_final: 0.6529 (m-30) REVERT: K 181 PHE cc_start: 0.6193 (m-10) cc_final: 0.5599 (m-10) REVERT: K 224 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7871 (pttm) REVERT: K 361 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7334 (mm-30) REVERT: K 398 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7512 (mm-30) REVERT: L 16 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7201 (mm-40) REVERT: L 17 ASN cc_start: 0.8047 (t0) cc_final: 0.7422 (t0) REVERT: L 43 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7569 (mptt) REVERT: L 73 ASP cc_start: 0.6965 (t0) cc_final: 0.6530 (m-30) REVERT: L 181 PHE cc_start: 0.6119 (m-10) cc_final: 0.5622 (m-80) outliers start: 64 outliers final: 53 residues processed: 593 average time/residue: 0.7893 time to fit residues: 567.4033 Evaluate side-chains 602 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 543 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 390 GLU Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 375 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 224 LYS Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 375 MET Chi-restraints excluded: chain L residue 383 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 298 optimal weight: 0.2980 chunk 211 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 399 optimal weight: 7.9990 chunk 414 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 503 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161941 restraints weight = 45174.873| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.39 r_work: 0.3822 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 42396 Z= 0.134 Angle : 0.616 59.200 57504 Z= 0.335 Chirality : 0.042 0.472 6300 Planarity : 0.004 0.038 7512 Dihedral : 4.180 32.197 5724 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.43 % Allowed : 16.95 % Favored : 81.62 % Cbeta Deviations : 0.02 % 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: 0.43 (0.12), residues: 5292 helix: 1.95 (0.11), residues: 2064 sheet: -0.91 (0.19), residues: 768 loop : -0.74 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 283 TYR 0.015 0.001 TYR I 285 PHE 0.016 0.001 PHE G 414 TRP 0.008 0.001 TRP C 77 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00301 (42396) covalent geometry : angle 0.61602 (57504) hydrogen bonds : bond 0.03398 ( 1967) hydrogen bonds : angle 4.34397 ( 5721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15100.87 seconds wall clock time: 257 minutes 57.29 seconds (15477.29 seconds total)