Starting phenix.real_space_refine on Mon Sep 14 17:15:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u8n_20688/09_2026/6u8n_20688.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8n_20688/09_2026/6u8n_20688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6u8n_20688/09_2026/6u8n_20688.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u8n_20688/09_2026/6u8n_20688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u8n_20688/09_2026/6u8n_20688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8n_20688/09_2026/6u8n_20688.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8n_20688/09_2026/6u8n_20688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8n_20688/09_2026/6u8n_20688.cif" } resolution = 3.29 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= 0.073 sd= 2.647 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 176 5.16 5 C 19656 2.51 5 N 5400 2.21 5 O 6224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31528 Number of models: 1 Model: "" Number of chains: 24 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "D" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 6.23, per 1000 atoms: 0.20 Number of scatterers: 31528 At special positions: 0 Unit cell: (156.45, 156.45, 141.75, 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 176 16.00 P 72 15.00 O 6224 8.00 N 5400 7.00 C 19656 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.3 seconds 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 48 sheets defined 37.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'I' and resid 1 through 6 Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.775A pdb=" N ASN A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 4.069A pdb=" N GLU A 177 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 225 through 228 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.721A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.517A pdb=" N ILE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.562A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 4.069A pdb=" N GLU B 177 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 225 through 228 Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.722A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.517A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.560A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'C' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.906A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 4.067A pdb=" N GLU C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 178 " --> pdb=" O LEU C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 178' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 225 through 228 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.721A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.518A pdb=" N ILE C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.999A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'D' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 4.068A pdb=" N GLU D 177 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE D 178 " --> pdb=" O LEU D 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 178' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 225 through 228 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.722A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.518A pdb=" N ILE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'M' and resid 2 through 6 Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN E 25 " --> pdb=" O GLN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 4.068A pdb=" N GLU E 177 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE E 178 " --> pdb=" O LEU E 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 178' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 225 through 228 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.722A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.518A pdb=" N ILE E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.999A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 420 Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'F' and resid 19 through 25 removed outlier: 3.775A pdb=" N ASN F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 137 removed outlier: 4.412A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.069A pdb=" N GLU F 177 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE F 178 " --> pdb=" O LEU F 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 178' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 225 through 228 Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.722A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.517A pdb=" N ILE F 284 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'G' and resid 19 through 25 removed outlier: 3.776A pdb=" N ASN G 25 " --> pdb=" O GLN G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 4.068A pdb=" N GLU G 177 " --> pdb=" O PHE G 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE G 178 " --> pdb=" O LEU G 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 174 through 178' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 225 through 228 Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.721A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.517A pdb=" N ILE G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 420 Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'P' and resid 2 through 6 Processing helix chain 'H' and resid 19 through 25 removed outlier: 3.775A pdb=" N ASN H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.907A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 110 removed outlier: 3.538A pdb=" N GLN H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 137 removed outlier: 4.411A pdb=" N VAL H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 178 removed outlier: 4.069A pdb=" N GLU H 177 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE H 178 " --> pdb=" O LEU H 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 174 through 178' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 225 through 228 Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.721A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.518A pdb=" N ILE H 284 " --> pdb=" O SER H 280 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 356 removed outlier: 3.561A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.998A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 420 Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY A 302 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.930A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 removed outlier: 4.165A pdb=" N SER A 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.690A pdb=" N SER A 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER D 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.484A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY B 302 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 removed outlier: 4.171A pdb=" N SER B 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY C 302 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 Processing sheet with id=AB9, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 401 through 403 removed outlier: 4.174A pdb=" N SER C 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.484A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY D 302 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.928A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY E 302 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 Processing sheet with id=AD2, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 403 removed outlier: 4.173A pdb=" N SER E 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.685A pdb=" N SER E 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER H 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 66 removed outlier: 6.484A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY F 302 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 401 through 403 removed outlier: 4.169A pdb=" N SER F 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY G 302 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.930A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 403 removed outlier: 4.167A pdb=" N SER G 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 66 removed outlier: 6.483A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY H 302 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 Processing sheet with id=AF3, first strand: chain 'H' and resid 188 through 189 removed outlier: 6.929A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) 1009 hydrogen bonds defined for protein. 2835 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: 5.86 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5285 1.30 - 1.42: 7683 1.42 - 1.55: 18572 1.55 - 1.68: 228 1.68 - 1.80: 304 Bond restraints: 32072 Sorted by residual: bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP D 601 " pdb=" C3' ATP D 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.82e+02 bond pdb=" C2' ATP F 601 " pdb=" C3' ATP F 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 ... (remaining 32067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 41995 4.27 - 8.55: 1192 8.55 - 12.82: 189 12.82 - 17.10: 53 17.10 - 21.37: 59 Bond angle restraints: 43488 Sorted by residual: angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 118.50 21.37 1.00e+00 1.00e+00 4.57e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 118.54 21.33 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 118.54 21.33 1.00e+00 1.00e+00 4.55e+02 ... (remaining 43483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 16824 16.34 - 32.69: 1520 32.69 - 49.03: 392 49.03 - 65.37: 208 65.37 - 81.72: 16 Dihedral angle restraints: 18960 sinusoidal: 7552 harmonic: 11408 Sorted by residual: dihedral pdb=" CA ILE F 437 " pdb=" C ILE F 437 " pdb=" N LYS F 438 " pdb=" CA LYS F 438 " ideal model delta harmonic sigma weight residual -180.00 -142.81 -37.19 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA ILE A 437 " pdb=" C ILE A 437 " pdb=" N LYS A 438 " pdb=" CA LYS A 438 " ideal model delta harmonic sigma weight residual -180.00 -142.81 -37.19 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA ILE E 437 " pdb=" C ILE E 437 " pdb=" N LYS E 438 " pdb=" CA LYS E 438 " ideal model delta harmonic sigma weight residual 180.00 -142.82 -37.18 0 5.00e+00 4.00e-02 5.53e+01 ... (remaining 18957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3024 0.064 - 0.127: 1404 0.127 - 0.191: 349 0.191 - 0.254: 150 0.254 - 0.318: 41 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CB VAL O 13 " pdb=" CA VAL O 13 " pdb=" CG1 VAL O 13 " pdb=" CG2 VAL O 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL M 13 " pdb=" CA VAL M 13 " pdb=" CG1 VAL M 13 " pdb=" CG2 VAL M 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL I 13 " pdb=" CA VAL I 13 " pdb=" CG1 VAL I 13 " pdb=" CG2 VAL I 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 4965 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 108 " -0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS H 108 " 0.070 2.00e-02 2.50e+03 pdb=" O LYS H 108 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS H 109 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 108 " 0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS F 108 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS F 108 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS F 109 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 108 " -0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C LYS E 108 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS E 108 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS E 109 " -0.024 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8896 2.79 - 3.32: 30144 3.32 - 3.84: 54335 3.84 - 4.37: 63420 4.37 - 4.90: 102989 Nonbonded interactions: 259784 Sorted by model distance: nonbonded pdb=" O ALA B 83 " pdb=" OG SER B 237 " model vdw 2.260 3.040 nonbonded pdb=" O ALA G 83 " pdb=" OG SER G 237 " model vdw 2.260 3.040 nonbonded pdb=" O ALA A 83 " pdb=" OG SER A 237 " model vdw 2.260 3.040 nonbonded pdb=" O ALA E 83 " pdb=" OG SER E 237 " model vdw 2.260 3.040 nonbonded pdb=" O ALA H 83 " pdb=" OG SER H 237 " model vdw 2.260 3.040 ... (remaining 259779 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: 0.11 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.710 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.020 0.377 32096 Z= 1.241 Angle : 1.900 21.373 43488 Z= 1.164 Chirality : 0.083 0.318 4968 Planarity : 0.007 0.044 5448 Dihedral : 15.099 81.715 11680 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.27 % Favored : 91.33 % Rotamer: Outliers : 9.05 % Allowed : 8.68 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.35 (0.11), residues: 3968 helix: -3.54 (0.09), residues: 1272 sheet: -2.60 (0.17), residues: 632 loop : -2.50 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG B 128 TYR 0.033 0.004 TYR H 484 PHE 0.022 0.005 PHE A 131 HIS 0.005 0.002 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01872 / 1.09 (32072) covalent geometry : angle 1.89977 / 1.16 (43488) hydrogen bonds : bond 0.18170 / 11.92 ( 1009) hydrogen bonds : angle 8.17454 / 5.52 ( 2835) Misc. bond : bond 0.21720 / 13.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 1065 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8308 (t0) cc_final: 0.8050 (t0) REVERT: A 75 GLU cc_start: 0.6903 (pm20) cc_final: 0.6458 (pm20) REVERT: A 105 ARG cc_start: 0.8259 (mtm110) cc_final: 0.8023 (ttp80) REVERT: A 132 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: A 137 HIS cc_start: 0.8230 (m90) cc_final: 0.7973 (m-70) REVERT: A 157 ILE cc_start: 0.9101 (mm) cc_final: 0.8759 (mm) REVERT: A 179 MET cc_start: 0.7808 (pp-130) cc_final: 0.6938 (ppp) REVERT: A 198 ASN cc_start: 0.9205 (m-40) cc_final: 0.8666 (m-40) REVERT: A 203 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8262 (ttp-110) REVERT: A 209 LEU cc_start: 0.7847 (tt) cc_final: 0.7636 (tt) REVERT: A 214 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7963 (tm-30) REVERT: A 256 ASP cc_start: 0.8332 (p0) cc_final: 0.7620 (p0) REVERT: A 272 VAL cc_start: 0.8882 (t) cc_final: 0.8526 (m) REVERT: A 277 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8516 (tm-30) REVERT: A 319 ASP cc_start: 0.8203 (m-30) cc_final: 0.7771 (m-30) REVERT: A 327 SER cc_start: 0.8666 (p) cc_final: 0.8390 (p) REVERT: A 352 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8328 (tm-30) REVERT: A 412 ARG cc_start: 0.8430 (ttp80) cc_final: 0.7944 (ptt90) REVERT: A 496 SER cc_start: 0.9130 (p) cc_final: 0.8924 (p) REVERT: A 507 HIS cc_start: 0.8540 (t-90) cc_final: 0.7900 (t-90) REVERT: B 16 ASP cc_start: 0.8347 (t0) cc_final: 0.8142 (t0) REVERT: B 28 ASP cc_start: 0.8239 (m-30) cc_final: 0.8020 (m-30) REVERT: B 75 GLU cc_start: 0.6891 (pm20) cc_final: 0.6496 (pm20) REVERT: B 105 ARG cc_start: 0.8275 (mtm110) cc_final: 0.8050 (ttp80) REVERT: B 132 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8641 (pt0) REVERT: B 137 HIS cc_start: 0.8215 (m90) cc_final: 0.7961 (m-70) REVERT: B 157 ILE cc_start: 0.9145 (mm) cc_final: 0.8807 (mm) REVERT: B 179 MET cc_start: 0.7965 (pp-130) cc_final: 0.7109 (ppp) REVERT: B 198 ASN cc_start: 0.9110 (m-40) cc_final: 0.8563 (m-40) REVERT: B 199 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7812 (tp30) REVERT: B 203 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8172 (ttp-110) REVERT: B 206 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8283 (mtmm) REVERT: B 214 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8032 (tm-30) REVERT: B 256 ASP cc_start: 0.8383 (p0) cc_final: 0.7737 (p0) REVERT: B 277 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 319 ASP cc_start: 0.8226 (m-30) cc_final: 0.7976 (m-30) REVERT: B 327 SER cc_start: 0.8622 (p) cc_final: 0.8371 (p) REVERT: B 352 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 412 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8005 (ptt90) REVERT: B 470 ASP cc_start: 0.8947 (m-30) cc_final: 0.8720 (m-30) REVERT: B 496 SER cc_start: 0.9106 (p) cc_final: 0.8858 (p) REVERT: B 507 HIS cc_start: 0.8517 (t-90) cc_final: 0.7873 (t-90) REVERT: C 16 ASP cc_start: 0.8297 (t0) cc_final: 0.8051 (t0) REVERT: C 75 GLU cc_start: 0.6894 (pm20) cc_final: 0.6467 (pm20) REVERT: C 105 ARG cc_start: 0.8307 (mtm110) cc_final: 0.8070 (ttp80) REVERT: C 132 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8679 (pt0) REVERT: C 157 ILE cc_start: 0.9093 (mm) cc_final: 0.8784 (mm) REVERT: C 179 MET cc_start: 0.7783 (pp-130) cc_final: 0.7016 (ppp) REVERT: C 198 ASN cc_start: 0.9136 (m-40) cc_final: 0.8581 (m-40) REVERT: C 203 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8207 (ttp-110) REVERT: C 209 LEU cc_start: 0.7805 (tt) cc_final: 0.7596 (tt) REVERT: C 214 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7955 (tm-30) REVERT: C 256 ASP cc_start: 0.8384 (p0) cc_final: 0.7744 (p0) REVERT: C 277 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8467 (tm-30) REVERT: C 300 ILE cc_start: 0.8455 (mm) cc_final: 0.8238 (mm) REVERT: C 319 ASP cc_start: 0.8296 (m-30) cc_final: 0.7852 (m-30) REVERT: C 327 SER cc_start: 0.8612 (p) cc_final: 0.8334 (p) REVERT: C 352 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 412 ARG cc_start: 0.8426 (ttp80) cc_final: 0.7985 (ptt90) REVERT: C 496 SER cc_start: 0.9078 (p) cc_final: 0.8843 (p) REVERT: C 507 HIS cc_start: 0.8539 (t-90) cc_final: 0.7883 (t-90) REVERT: D 16 ASP cc_start: 0.8277 (t0) cc_final: 0.8013 (t0) REVERT: D 34 ASP cc_start: 0.9071 (t0) cc_final: 0.8822 (t0) REVERT: D 75 GLU cc_start: 0.7034 (pm20) cc_final: 0.6644 (pm20) REVERT: D 105 ARG cc_start: 0.8312 (mtm110) cc_final: 0.8055 (ttp80) REVERT: D 121 LEU cc_start: 0.8348 (mm) cc_final: 0.8147 (mp) REVERT: D 132 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: D 137 HIS cc_start: 0.8221 (m90) cc_final: 0.7973 (m-70) REVERT: D 157 ILE cc_start: 0.9145 (mm) cc_final: 0.8805 (mm) REVERT: D 179 MET cc_start: 0.7989 (pp-130) cc_final: 0.7109 (ppp) REVERT: D 198 ASN cc_start: 0.9186 (m-40) cc_final: 0.8624 (m-40) REVERT: D 203 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8096 (mtp-110) REVERT: D 214 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7980 (tm-30) REVERT: D 277 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8443 (tm-30) REVERT: D 286 MET cc_start: 0.8991 (tmt) cc_final: 0.8502 (tmt) REVERT: D 319 ASP cc_start: 0.8204 (m-30) cc_final: 0.7958 (m-30) REVERT: D 327 SER cc_start: 0.8646 (p) cc_final: 0.8403 (p) REVERT: D 352 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8373 (tm-30) REVERT: D 412 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8006 (ptt90) REVERT: D 470 ASP cc_start: 0.8881 (m-30) cc_final: 0.8678 (m-30) REVERT: D 507 HIS cc_start: 0.8567 (t-90) cc_final: 0.7914 (t-90) REVERT: E 26 CYS cc_start: 0.8516 (m) cc_final: 0.8315 (t) REVERT: E 34 ASP cc_start: 0.9042 (t0) cc_final: 0.8836 (t0) REVERT: E 75 GLU cc_start: 0.6940 (pm20) cc_final: 0.6515 (pm20) REVERT: E 105 ARG cc_start: 0.8244 (mtm110) cc_final: 0.8030 (ttp80) REVERT: E 132 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8658 (pt0) REVERT: E 137 HIS cc_start: 0.8304 (m90) cc_final: 0.8078 (m-70) REVERT: E 157 ILE cc_start: 0.9089 (mm) cc_final: 0.8803 (mm) REVERT: E 173 CYS cc_start: 0.7451 (p) cc_final: 0.6880 (p) REVERT: E 179 MET cc_start: 0.7828 (pp-130) cc_final: 0.7096 (ppp) REVERT: E 198 ASN cc_start: 0.9123 (m-40) cc_final: 0.8624 (m-40) REVERT: E 203 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8205 (ttp-110) REVERT: E 214 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7999 (tm-30) REVERT: E 256 ASP cc_start: 0.8280 (p0) cc_final: 0.7572 (p0) REVERT: E 272 VAL cc_start: 0.8852 (t) cc_final: 0.8572 (m) REVERT: E 277 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8463 (tm-30) REVERT: E 300 ILE cc_start: 0.8448 (mm) cc_final: 0.8235 (mm) REVERT: E 319 ASP cc_start: 0.8241 (m-30) cc_final: 0.7808 (m-30) REVERT: E 327 SER cc_start: 0.8587 (p) cc_final: 0.8319 (p) REVERT: E 352 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8351 (tm-30) REVERT: E 412 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8014 (ptt90) REVERT: E 496 SER cc_start: 0.9038 (p) cc_final: 0.8782 (p) REVERT: E 507 HIS cc_start: 0.8549 (t-90) cc_final: 0.7919 (t-90) REVERT: F 16 ASP cc_start: 0.8245 (t0) cc_final: 0.8023 (t0) REVERT: F 28 ASP cc_start: 0.8305 (m-30) cc_final: 0.8079 (m-30) REVERT: F 75 GLU cc_start: 0.7022 (pm20) cc_final: 0.6650 (pm20) REVERT: F 105 ARG cc_start: 0.8311 (mtm110) cc_final: 0.8019 (ttp80) REVERT: F 121 LEU cc_start: 0.8335 (mm) cc_final: 0.8131 (mp) REVERT: F 132 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: F 137 HIS cc_start: 0.8261 (m90) cc_final: 0.7997 (m-70) REVERT: F 157 ILE cc_start: 0.9143 (mm) cc_final: 0.8805 (mm) REVERT: F 179 MET cc_start: 0.7934 (pp-130) cc_final: 0.7053 (ppp) REVERT: F 198 ASN cc_start: 0.9145 (m-40) cc_final: 0.8696 (m-40) REVERT: F 199 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: F 203 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8064 (ttp-110) REVERT: F 209 LEU cc_start: 0.7876 (tt) cc_final: 0.7671 (tt) REVERT: F 214 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7909 (tm-30) REVERT: F 277 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8412 (tm-30) REVERT: F 286 MET cc_start: 0.8992 (tmt) cc_final: 0.8527 (tmt) REVERT: F 319 ASP cc_start: 0.8222 (m-30) cc_final: 0.7836 (m-30) REVERT: F 327 SER cc_start: 0.8665 (p) cc_final: 0.8428 (p) REVERT: F 352 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8397 (tm-30) REVERT: F 412 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8008 (ptt90) REVERT: F 470 ASP cc_start: 0.8901 (m-30) cc_final: 0.8701 (m-30) REVERT: F 496 SER cc_start: 0.9005 (p) cc_final: 0.8788 (p) REVERT: F 507 HIS cc_start: 0.8560 (t-90) cc_final: 0.7933 (t-90) REVERT: G 16 ASP cc_start: 0.8301 (t0) cc_final: 0.8086 (t0) REVERT: G 34 ASP cc_start: 0.9063 (t0) cc_final: 0.8851 (t0) REVERT: G 75 GLU cc_start: 0.6973 (pm20) cc_final: 0.6562 (pm20) REVERT: G 105 ARG cc_start: 0.8287 (mtm110) cc_final: 0.8008 (ttp80) REVERT: G 137 HIS cc_start: 0.8198 (m90) cc_final: 0.7920 (m-70) REVERT: G 157 ILE cc_start: 0.9107 (mm) cc_final: 0.8787 (mm) REVERT: G 179 MET cc_start: 0.7840 (pp-130) cc_final: 0.7099 (ppp) REVERT: G 198 ASN cc_start: 0.9137 (m-40) cc_final: 0.8691 (m-40) REVERT: G 209 LEU cc_start: 0.7774 (tt) cc_final: 0.7566 (tt) REVERT: G 214 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7897 (tm-30) REVERT: G 272 VAL cc_start: 0.8926 (t) cc_final: 0.8541 (m) REVERT: G 277 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8577 (tm-30) REVERT: G 286 MET cc_start: 0.8942 (tmt) cc_final: 0.8330 (tmt) REVERT: G 319 ASP cc_start: 0.8222 (m-30) cc_final: 0.7781 (m-30) REVERT: G 327 SER cc_start: 0.8613 (p) cc_final: 0.8323 (p) REVERT: G 352 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8394 (tm-30) REVERT: G 412 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8015 (ptt90) REVERT: G 496 SER cc_start: 0.9134 (p) cc_final: 0.8909 (p) REVERT: G 507 HIS cc_start: 0.8564 (t-90) cc_final: 0.7915 (t-90) REVERT: H 16 ASP cc_start: 0.8374 (t0) cc_final: 0.8112 (t0) REVERT: H 28 ASP cc_start: 0.8245 (m-30) cc_final: 0.8017 (m-30) REVERT: H 75 GLU cc_start: 0.6947 (pm20) cc_final: 0.6552 (pm20) REVERT: H 105 ARG cc_start: 0.8280 (mtm110) cc_final: 0.8047 (ttp80) REVERT: H 137 HIS cc_start: 0.8215 (m90) cc_final: 0.7964 (m-70) REVERT: H 157 ILE cc_start: 0.9148 (mm) cc_final: 0.8826 (mm) REVERT: H 179 MET cc_start: 0.8062 (pp-130) cc_final: 0.7235 (ppp) REVERT: H 198 ASN cc_start: 0.9087 (m-40) cc_final: 0.8624 (m-40) REVERT: H 203 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8173 (ttp-110) REVERT: H 214 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8001 (tm-30) REVERT: H 272 VAL cc_start: 0.8927 (t) cc_final: 0.8604 (m) REVERT: H 277 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8364 (tm-30) REVERT: H 286 MET cc_start: 0.8977 (tmt) cc_final: 0.8481 (tmt) REVERT: H 319 ASP cc_start: 0.8184 (m-30) cc_final: 0.7938 (m-30) REVERT: H 327 SER cc_start: 0.8619 (p) cc_final: 0.8286 (p) REVERT: H 352 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8292 (tm-30) REVERT: H 412 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7993 (ptt90) REVERT: H 470 ASP cc_start: 0.8938 (m-30) cc_final: 0.8727 (m-30) REVERT: H 496 SER cc_start: 0.9094 (p) cc_final: 0.8802 (p) REVERT: H 507 HIS cc_start: 0.8540 (t-90) cc_final: 0.7894 (t-90) outliers start: 296 outliers final: 107 residues processed: 1203 average time/residue: 0.2141 time to fit residues: 405.7382 Evaluate side-chains 857 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 742 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 126 ARG Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 399 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 126 ARG Chi-restraints excluded: chain G residue 199 GLU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 199 GLU Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 399 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 HIS A 112 GLN A 198 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 343 GLN A 478 GLN B 93 HIS B 198 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 343 GLN B 454 HIS B 478 GLN C 112 GLN C 198 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 343 GLN C 454 HIS C 478 GLN D 198 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 343 GLN D 454 HIS D 478 GLN E 21 GLN E 25 ASN E 93 HIS E 112 GLN E 198 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 454 HIS E 478 GLN F 198 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 343 GLN F 454 HIS F 478 GLN G 112 GLN G 198 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 478 GLN H 93 HIS H 198 ASN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN H 454 HIS H 478 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102218 restraints weight = 54549.671| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.68 r_work: 0.3065 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32096 Z= 0.153 Angle : 0.796 8.734 43488 Z= 0.402 Chirality : 0.049 0.201 4968 Planarity : 0.004 0.039 5448 Dihedral : 10.649 59.950 4690 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.96 % Favored : 92.64 % Rotamer: Outliers : 5.96 % Allowed : 15.71 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -3.04 (0.12), residues: 3968 helix: -2.03 (0.12), residues: 1272 sheet: -1.84 (0.21), residues: 544 loop : -2.04 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 126 TYR 0.012 0.001 TYR C 348 PHE 0.015 0.001 PHE F 401 HIS 0.003 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (32072) covalent geometry : angle 0.79613 / 0.40 (43488) hydrogen bonds : bond 0.03854 / 2.50 ( 1009) hydrogen bonds : angle 5.76232 / 3.89 ( 2835) Misc. bond : bond 0.00104 / 0.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 967 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8940 (m-40) cc_final: 0.8606 (p0) REVERT: A 36 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8385 (pp) REVERT: A 75 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: A 105 ARG cc_start: 0.8305 (mtm110) cc_final: 0.8087 (ttp80) REVERT: A 137 HIS cc_start: 0.8111 (m90) cc_final: 0.7708 (m-70) REVERT: A 179 MET cc_start: 0.7772 (pp-130) cc_final: 0.6522 (ppp) REVERT: A 198 ASN cc_start: 0.9221 (m110) cc_final: 0.8666 (m-40) REVERT: A 199 GLU cc_start: 0.8116 (pt0) cc_final: 0.7860 (tp30) REVERT: A 202 GLN cc_start: 0.8324 (pp30) cc_final: 0.7812 (pp30) REVERT: A 209 LEU cc_start: 0.8133 (tt) cc_final: 0.7933 (tt) REVERT: A 214 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8021 (tm-30) REVERT: A 245 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8241 (mm) REVERT: A 256 ASP cc_start: 0.8555 (p0) cc_final: 0.8175 (p0) REVERT: A 319 ASP cc_start: 0.8553 (m-30) cc_final: 0.8255 (m-30) REVERT: A 327 SER cc_start: 0.8798 (p) cc_final: 0.8432 (p) REVERT: A 352 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 353 TYR cc_start: 0.8948 (t80) cc_final: 0.8666 (t80) REVERT: A 412 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7235 (tmm-80) REVERT: A 420 MET cc_start: 0.6862 (mtm) cc_final: 0.6639 (mtm) REVERT: A 455 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8566 (mmmm) REVERT: A 474 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8557 (mtpt) REVERT: A 483 MET cc_start: 0.9301 (tmm) cc_final: 0.8713 (tmm) REVERT: A 496 SER cc_start: 0.9085 (p) cc_final: 0.8799 (p) REVERT: A 507 HIS cc_start: 0.8826 (t-90) cc_final: 0.8381 (t-90) REVERT: B 16 ASP cc_start: 0.8441 (t0) cc_final: 0.8220 (t0) REVERT: B 25 ASN cc_start: 0.8810 (m-40) cc_final: 0.8554 (p0) REVERT: B 36 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8382 (pp) REVERT: B 75 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: B 105 ARG cc_start: 0.8304 (mtm110) cc_final: 0.8075 (ttp80) REVERT: B 179 MET cc_start: 0.7926 (pp-130) cc_final: 0.6725 (ppp) REVERT: B 198 ASN cc_start: 0.9227 (m110) cc_final: 0.8645 (m-40) REVERT: B 199 GLU cc_start: 0.8130 (pt0) cc_final: 0.7868 (tp30) REVERT: B 205 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8412 (ttmm) REVERT: B 206 LYS cc_start: 0.8346 (mtpp) cc_final: 0.7945 (mtmm) REVERT: B 214 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8230 (tm-30) REVERT: B 245 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8232 (mm) REVERT: B 273 LEU cc_start: 0.8985 (mp) cc_final: 0.8754 (mt) REVERT: B 319 ASP cc_start: 0.8663 (m-30) cc_final: 0.8346 (m-30) REVERT: B 327 SER cc_start: 0.8743 (p) cc_final: 0.8229 (p) REVERT: B 352 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 353 TYR cc_start: 0.9068 (t80) cc_final: 0.8797 (t80) REVERT: B 412 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7466 (ptt90) REVERT: B 420 MET cc_start: 0.6830 (mtm) cc_final: 0.6625 (mtm) REVERT: B 461 ILE cc_start: 0.8918 (pp) cc_final: 0.8587 (mt) REVERT: B 507 HIS cc_start: 0.8785 (t-90) cc_final: 0.8350 (t-90) REVERT: C 16 ASP cc_start: 0.8537 (t0) cc_final: 0.8328 (t0) REVERT: C 36 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8404 (pp) REVERT: C 75 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: C 105 ARG cc_start: 0.8354 (mtm110) cc_final: 0.8071 (ttp80) REVERT: C 174 PHE cc_start: 0.8381 (m-80) cc_final: 0.8081 (t80) REVERT: C 179 MET cc_start: 0.7663 (pp-130) cc_final: 0.6440 (ppp) REVERT: C 198 ASN cc_start: 0.9184 (m110) cc_final: 0.8572 (m-40) REVERT: C 199 GLU cc_start: 0.8112 (pt0) cc_final: 0.7745 (tp30) REVERT: C 203 ARG cc_start: 0.8722 (tpp-160) cc_final: 0.8039 (mtp-110) REVERT: C 205 LYS cc_start: 0.9134 (mtpp) cc_final: 0.8532 (ttmm) REVERT: C 209 LEU cc_start: 0.8153 (tt) cc_final: 0.7926 (tt) REVERT: C 214 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8086 (tm-30) REVERT: C 245 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8145 (mm) REVERT: C 274 ASP cc_start: 0.8849 (t0) cc_final: 0.8648 (t0) REVERT: C 319 ASP cc_start: 0.8617 (m-30) cc_final: 0.8307 (m-30) REVERT: C 327 SER cc_start: 0.8741 (p) cc_final: 0.8458 (p) REVERT: C 352 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8615 (tm-30) REVERT: C 353 TYR cc_start: 0.9020 (t80) cc_final: 0.8762 (t80) REVERT: C 412 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7451 (ptt90) REVERT: C 420 MET cc_start: 0.6843 (mtm) cc_final: 0.6630 (mtm) REVERT: C 455 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8596 (mmmm) REVERT: C 474 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8507 (mtpt) REVERT: C 507 HIS cc_start: 0.8846 (t-90) cc_final: 0.8402 (t-90) REVERT: D 16 ASP cc_start: 0.8560 (t0) cc_final: 0.8338 (t0) REVERT: D 36 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8467 (pp) REVERT: D 75 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: D 105 ARG cc_start: 0.8365 (mtm110) cc_final: 0.8096 (ttp80) REVERT: D 137 HIS cc_start: 0.8127 (m90) cc_final: 0.7739 (m-70) REVERT: D 174 PHE cc_start: 0.8196 (m-80) cc_final: 0.7548 (t80) REVERT: D 179 MET cc_start: 0.8034 (pp-130) cc_final: 0.6888 (ppp) REVERT: D 198 ASN cc_start: 0.9244 (m110) cc_final: 0.8707 (m-40) REVERT: D 199 GLU cc_start: 0.8151 (pt0) cc_final: 0.7870 (tp30) REVERT: D 202 GLN cc_start: 0.8409 (pp30) cc_final: 0.7924 (pp30) REVERT: D 205 LYS cc_start: 0.9102 (mtpp) cc_final: 0.8472 (ttmm) REVERT: D 214 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8148 (tm-30) REVERT: D 245 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8289 (mm) REVERT: D 286 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8764 (tmt) REVERT: D 319 ASP cc_start: 0.8576 (m-30) cc_final: 0.8275 (m-30) REVERT: D 327 SER cc_start: 0.8818 (p) cc_final: 0.8508 (p) REVERT: D 352 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 353 TYR cc_start: 0.9023 (t80) cc_final: 0.8758 (t80) REVERT: D 412 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7267 (tmm-80) REVERT: D 420 MET cc_start: 0.6799 (mtm) cc_final: 0.6579 (mtm) REVERT: D 455 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8621 (mmmm) REVERT: D 474 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8545 (mtpt) REVERT: D 507 HIS cc_start: 0.8842 (t-90) cc_final: 0.8396 (t-90) REVERT: E 25 ASN cc_start: 0.8871 (m110) cc_final: 0.8565 (p0) REVERT: E 26 CYS cc_start: 0.8923 (m) cc_final: 0.8628 (t) REVERT: E 34 ASP cc_start: 0.9146 (t0) cc_final: 0.8944 (t0) REVERT: E 75 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6719 (pm20) REVERT: E 179 MET cc_start: 0.7743 (pp-130) cc_final: 0.6425 (ppp) REVERT: E 198 ASN cc_start: 0.9194 (m110) cc_final: 0.8616 (m-40) REVERT: E 199 GLU cc_start: 0.8114 (pt0) cc_final: 0.7701 (tp30) REVERT: E 202 GLN cc_start: 0.8331 (pp30) cc_final: 0.7893 (pp30) REVERT: E 203 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8006 (mtp-110) REVERT: E 205 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8482 (ttmm) REVERT: E 209 LEU cc_start: 0.8066 (tt) cc_final: 0.7839 (tt) REVERT: E 214 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8175 (tm-30) REVERT: E 245 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8210 (mm) REVERT: E 256 ASP cc_start: 0.8322 (p0) cc_final: 0.7956 (p0) REVERT: E 327 SER cc_start: 0.8716 (p) cc_final: 0.8488 (p) REVERT: E 352 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8574 (tm-30) REVERT: E 412 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7489 (ptt90) REVERT: E 420 MET cc_start: 0.6826 (mtm) cc_final: 0.6616 (mtm) REVERT: E 455 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (mmmm) REVERT: E 483 MET cc_start: 0.9338 (tmm) cc_final: 0.8746 (tmm) REVERT: E 496 SER cc_start: 0.9144 (p) cc_final: 0.8855 (p) REVERT: E 507 HIS cc_start: 0.8817 (t-90) cc_final: 0.8410 (t-90) REVERT: F 16 ASP cc_start: 0.8549 (t0) cc_final: 0.8304 (t0) REVERT: F 34 ASP cc_start: 0.9241 (t0) cc_final: 0.9019 (t0) REVERT: F 75 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: F 92 HIS cc_start: 0.9238 (p90) cc_final: 0.9038 (p-80) REVERT: F 174 PHE cc_start: 0.8011 (m-80) cc_final: 0.7310 (t80) REVERT: F 179 MET cc_start: 0.7898 (pp-130) cc_final: 0.6802 (ppp) REVERT: F 198 ASN cc_start: 0.9215 (m110) cc_final: 0.8670 (m-40) REVERT: F 199 GLU cc_start: 0.8076 (pt0) cc_final: 0.7626 (tp30) REVERT: F 202 GLN cc_start: 0.8331 (pp30) cc_final: 0.7896 (pp30) REVERT: F 203 ARG cc_start: 0.8623 (tpp-160) cc_final: 0.7981 (mtp-110) REVERT: F 205 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8542 (ttmm) REVERT: F 214 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8052 (tm-30) REVERT: F 245 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8161 (mm) REVERT: F 256 ASP cc_start: 0.8424 (p0) cc_final: 0.8193 (p0) REVERT: F 286 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8823 (tmt) REVERT: F 319 ASP cc_start: 0.8575 (m-30) cc_final: 0.8274 (m-30) REVERT: F 327 SER cc_start: 0.8754 (p) cc_final: 0.8514 (p) REVERT: F 352 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8571 (tm-30) REVERT: F 353 TYR cc_start: 0.9046 (t80) cc_final: 0.8793 (t80) REVERT: F 412 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7263 (tmm-80) REVERT: F 420 MET cc_start: 0.6753 (mtm) cc_final: 0.6523 (mtm) REVERT: F 455 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8681 (mmmm) REVERT: F 474 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8476 (mtpt) REVERT: F 483 MET cc_start: 0.9275 (tmm) cc_final: 0.8661 (tmm) REVERT: F 507 HIS cc_start: 0.8869 (t-90) cc_final: 0.8430 (t-90) REVERT: G 75 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: G 105 ARG cc_start: 0.8393 (mtm110) cc_final: 0.8080 (ttp80) REVERT: G 174 PHE cc_start: 0.8006 (m-80) cc_final: 0.7679 (t80) REVERT: G 179 MET cc_start: 0.7757 (pp-130) cc_final: 0.6514 (ppp) REVERT: G 198 ASN cc_start: 0.9186 (m110) cc_final: 0.8647 (m-40) REVERT: G 199 GLU cc_start: 0.8104 (pt0) cc_final: 0.7743 (tp30) REVERT: G 202 GLN cc_start: 0.8472 (pp30) cc_final: 0.8137 (pp30) REVERT: G 203 ARG cc_start: 0.8746 (tpp-160) cc_final: 0.8003 (mtp-110) REVERT: G 214 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8000 (tm-30) REVERT: G 245 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8177 (mm) REVERT: G 259 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8233 (mtp180) REVERT: G 286 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8717 (tmt) REVERT: G 319 ASP cc_start: 0.8541 (m-30) cc_final: 0.8211 (m-30) REVERT: G 327 SER cc_start: 0.8741 (p) cc_final: 0.8460 (p) REVERT: G 352 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8540 (tm-30) REVERT: G 353 TYR cc_start: 0.8955 (t80) cc_final: 0.8716 (t80) REVERT: G 412 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7248 (tmm-80) REVERT: G 455 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8663 (mmmm) REVERT: G 474 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8569 (mtpt) REVERT: G 487 GLU cc_start: 0.8988 (tt0) cc_final: 0.8563 (tt0) REVERT: G 507 HIS cc_start: 0.8844 (t-90) cc_final: 0.8398 (t-90) REVERT: H 36 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8401 (pp) REVERT: H 75 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6631 (pm20) REVERT: H 105 ARG cc_start: 0.8351 (mtm110) cc_final: 0.8140 (ttp80) REVERT: H 179 MET cc_start: 0.8066 (pp-130) cc_final: 0.6940 (ppp) REVERT: H 198 ASN cc_start: 0.9218 (m110) cc_final: 0.8651 (m-40) REVERT: H 199 GLU cc_start: 0.8083 (pt0) cc_final: 0.7790 (tp30) REVERT: H 202 GLN cc_start: 0.8416 (pp30) cc_final: 0.7937 (pp30) REVERT: H 205 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8639 (mmmm) REVERT: H 214 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8124 (tm-30) REVERT: H 245 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8254 (mm) REVERT: H 256 ASP cc_start: 0.8436 (p0) cc_final: 0.8214 (p0) REVERT: H 286 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8770 (tmt) REVERT: H 319 ASP cc_start: 0.8614 (m-30) cc_final: 0.8291 (m-30) REVERT: H 352 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8513 (tm-30) REVERT: H 353 TYR cc_start: 0.9022 (t80) cc_final: 0.8756 (t80) REVERT: H 412 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7517 (ptt90) REVERT: H 483 MET cc_start: 0.9291 (tmm) cc_final: 0.8709 (tmm) REVERT: H 507 HIS cc_start: 0.8812 (t-90) cc_final: 0.8382 (t-90) outliers start: 195 outliers final: 101 residues processed: 1091 average time/residue: 0.1964 time to fit residues: 343.8810 Evaluate side-chains 922 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 790 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain J residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain N residue 11 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain O residue 11 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 212 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 218 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 281 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 391 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 chunk 369 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 387 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS D 92 HIS ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS E 21 GLN E 25 ASN E 102 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 HIS ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 HIS ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 HIS ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101282 restraints weight = 55001.953| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.71 r_work: 0.3060 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32096 Z= 0.165 Angle : 0.743 8.040 43488 Z= 0.378 Chirality : 0.049 0.167 4968 Planarity : 0.004 0.049 5448 Dihedral : 9.263 65.432 4556 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.24 % Favored : 91.73 % Rotamer: Outliers : 5.26 % Allowed : 20.42 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.29 (0.13), residues: 3968 helix: -1.03 (0.13), residues: 1288 sheet: -1.58 (0.22), residues: 528 loop : -1.80 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 493 TYR 0.011 0.001 TYR E 348 PHE 0.012 0.001 PHE E 24 HIS 0.003 0.001 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (32072) covalent geometry : angle 0.74348 / 0.38 (43488) hydrogen bonds : bond 0.03509 / 2.28 ( 1009) hydrogen bonds : angle 5.32652 / 3.61 ( 2835) Misc. bond : bond 0.00087 / 0.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 863 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8916 (m-40) cc_final: 0.8619 (p0) REVERT: A 75 GLU cc_start: 0.7062 (pm20) cc_final: 0.6435 (mp0) REVERT: A 100 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.9095 (pt0) REVERT: A 108 LYS cc_start: 0.8678 (tptp) cc_final: 0.8306 (tppt) REVERT: A 179 MET cc_start: 0.7838 (pp-130) cc_final: 0.6558 (ppp) REVERT: A 198 ASN cc_start: 0.9187 (m110) cc_final: 0.8707 (m-40) REVERT: A 199 GLU cc_start: 0.8144 (pt0) cc_final: 0.7783 (tp30) REVERT: A 202 GLN cc_start: 0.8487 (pp30) cc_final: 0.8038 (pp30) REVERT: A 203 ARG cc_start: 0.8730 (tpp-160) cc_final: 0.8191 (mtp-110) REVERT: A 209 LEU cc_start: 0.8113 (tt) cc_final: 0.7865 (tt) REVERT: A 214 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8078 (tm-30) REVERT: A 245 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8149 (mm) REVERT: A 274 ASP cc_start: 0.8974 (t0) cc_final: 0.8749 (t0) REVERT: A 279 ASN cc_start: 0.8561 (t0) cc_final: 0.8280 (t0) REVERT: A 319 ASP cc_start: 0.8548 (m-30) cc_final: 0.8283 (m-30) REVERT: A 352 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8515 (tm-30) REVERT: A 353 TYR cc_start: 0.8931 (t80) cc_final: 0.8668 (t80) REVERT: A 412 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7437 (ptt90) REVERT: A 420 MET cc_start: 0.6817 (mtm) cc_final: 0.6598 (mtm) REVERT: A 455 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8586 (mmmm) REVERT: A 474 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8665 (mtpt) REVERT: A 507 HIS cc_start: 0.8821 (t-90) cc_final: 0.8401 (t-90) REVERT: B 16 ASP cc_start: 0.8472 (t0) cc_final: 0.8229 (t0) REVERT: B 25 ASN cc_start: 0.8799 (m-40) cc_final: 0.8575 (p0) REVERT: B 75 GLU cc_start: 0.7040 (pm20) cc_final: 0.6585 (mp0) REVERT: B 108 LYS cc_start: 0.8593 (tptp) cc_final: 0.8207 (tppt) REVERT: B 150 MET cc_start: 0.7974 (ttt) cc_final: 0.7468 (tpp) REVERT: B 179 MET cc_start: 0.7921 (pp-130) cc_final: 0.6729 (ppp) REVERT: B 194 LEU cc_start: 0.8705 (mm) cc_final: 0.8264 (mm) REVERT: B 198 ASN cc_start: 0.9233 (m110) cc_final: 0.8659 (m-40) REVERT: B 199 GLU cc_start: 0.8113 (pt0) cc_final: 0.7797 (tp30) REVERT: B 202 GLN cc_start: 0.8402 (pp30) cc_final: 0.7912 (pp30) REVERT: B 205 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8423 (ttmm) REVERT: B 214 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8206 (tm-30) REVERT: B 245 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8155 (mm) REVERT: B 300 ILE cc_start: 0.8642 (mm) cc_final: 0.8303 (mm) REVERT: B 319 ASP cc_start: 0.8544 (m-30) cc_final: 0.8304 (m-30) REVERT: B 352 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 353 TYR cc_start: 0.9014 (t80) cc_final: 0.8787 (t80) REVERT: B 412 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7447 (ptt90) REVERT: B 420 MET cc_start: 0.6771 (mtm) cc_final: 0.6538 (mtm) REVERT: B 461 ILE cc_start: 0.8959 (pp) cc_final: 0.8659 (mt) REVERT: B 507 HIS cc_start: 0.8777 (t-90) cc_final: 0.8363 (t-90) REVERT: C 16 ASP cc_start: 0.8491 (t0) cc_final: 0.8288 (t0) REVERT: C 75 GLU cc_start: 0.7086 (pm20) cc_final: 0.6609 (mp0) REVERT: C 108 LYS cc_start: 0.8677 (tptp) cc_final: 0.8281 (tppt) REVERT: C 150 MET cc_start: 0.8120 (ttt) cc_final: 0.7545 (tpp) REVERT: C 174 PHE cc_start: 0.8361 (m-80) cc_final: 0.8012 (t80) REVERT: C 175 LEU cc_start: 0.8132 (mt) cc_final: 0.7645 (mt) REVERT: C 179 MET cc_start: 0.7679 (pp-130) cc_final: 0.6399 (ppp) REVERT: C 198 ASN cc_start: 0.9147 (m110) cc_final: 0.8592 (m-40) REVERT: C 199 GLU cc_start: 0.8124 (pt0) cc_final: 0.7746 (tp30) REVERT: C 202 GLN cc_start: 0.8395 (pp30) cc_final: 0.7965 (pp30) REVERT: C 203 ARG cc_start: 0.8841 (tpp-160) cc_final: 0.8190 (mtp-110) REVERT: C 205 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8457 (ttmm) REVERT: C 209 LEU cc_start: 0.8174 (tt) cc_final: 0.7956 (tt) REVERT: C 214 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8053 (tm-30) REVERT: C 245 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8106 (mm) REVERT: C 261 ASP cc_start: 0.9083 (m-30) cc_final: 0.8831 (m-30) REVERT: C 319 ASP cc_start: 0.8618 (m-30) cc_final: 0.8349 (m-30) REVERT: C 327 SER cc_start: 0.8591 (p) cc_final: 0.7990 (p) REVERT: C 352 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8599 (tm-30) REVERT: C 353 TYR cc_start: 0.8967 (t80) cc_final: 0.8718 (t80) REVERT: C 412 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7494 (ptt90) REVERT: C 420 MET cc_start: 0.6772 (mtm) cc_final: 0.6563 (mtm) REVERT: C 455 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8599 (mmmm) REVERT: C 474 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8562 (mtpt) REVERT: C 507 HIS cc_start: 0.8822 (t-90) cc_final: 0.8414 (t-90) REVERT: D 16 ASP cc_start: 0.8497 (t0) cc_final: 0.8262 (t0) REVERT: D 34 ASP cc_start: 0.9251 (t0) cc_final: 0.9019 (t0) REVERT: D 75 GLU cc_start: 0.7202 (pm20) cc_final: 0.6800 (pm20) REVERT: D 100 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.9096 (pt0) REVERT: D 105 ARG cc_start: 0.8345 (mtm110) cc_final: 0.8143 (ttp80) REVERT: D 108 LYS cc_start: 0.8635 (tptp) cc_final: 0.8265 (tppt) REVERT: D 179 MET cc_start: 0.8040 (pp-130) cc_final: 0.6898 (ppp) REVERT: D 198 ASN cc_start: 0.9239 (m110) cc_final: 0.8747 (m-40) REVERT: D 199 GLU cc_start: 0.8186 (pt0) cc_final: 0.7891 (tp30) REVERT: D 202 GLN cc_start: 0.8536 (pp30) cc_final: 0.8024 (pp30) REVERT: D 205 LYS cc_start: 0.9076 (mtpp) cc_final: 0.8375 (ttmm) REVERT: D 214 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8162 (tm-30) REVERT: D 244 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8311 (mt) REVERT: D 245 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8259 (mm) REVERT: D 300 ILE cc_start: 0.8855 (mm) cc_final: 0.8573 (mm) REVERT: D 319 ASP cc_start: 0.8556 (m-30) cc_final: 0.8351 (m-30) REVERT: D 327 SER cc_start: 0.8654 (p) cc_final: 0.8156 (p) REVERT: D 352 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8576 (tm-30) REVERT: D 353 TYR cc_start: 0.8993 (t80) cc_final: 0.8762 (t80) REVERT: D 412 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7498 (ptt90) REVERT: D 455 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8628 (mmmm) REVERT: D 474 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8614 (mtpt) REVERT: D 507 HIS cc_start: 0.8805 (t-90) cc_final: 0.8377 (t-90) REVERT: E 25 ASN cc_start: 0.8914 (m-40) cc_final: 0.8622 (p0) REVERT: E 26 CYS cc_start: 0.8974 (m) cc_final: 0.8578 (t) REVERT: E 75 GLU cc_start: 0.7099 (pm20) cc_final: 0.6614 (mp0) REVERT: E 108 LYS cc_start: 0.8689 (tptp) cc_final: 0.8286 (tppt) REVERT: E 179 MET cc_start: 0.7715 (pp-130) cc_final: 0.6453 (ppp) REVERT: E 198 ASN cc_start: 0.9165 (m110) cc_final: 0.8592 (m-40) REVERT: E 199 GLU cc_start: 0.8132 (pt0) cc_final: 0.7696 (tp30) REVERT: E 202 GLN cc_start: 0.8457 (pp30) cc_final: 0.8022 (pp30) REVERT: E 203 ARG cc_start: 0.8766 (tpp-160) cc_final: 0.8117 (mtp-110) REVERT: E 209 LEU cc_start: 0.8099 (tt) cc_final: 0.7866 (tt) REVERT: E 214 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8127 (tm-30) REVERT: E 244 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8369 (mt) REVERT: E 245 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8147 (mm) REVERT: E 261 ASP cc_start: 0.9067 (m-30) cc_final: 0.8786 (m-30) REVERT: E 319 ASP cc_start: 0.8632 (m-30) cc_final: 0.8345 (m-30) REVERT: E 325 MET cc_start: 0.8213 (ptm) cc_final: 0.7982 (ptm) REVERT: E 327 SER cc_start: 0.8713 (p) cc_final: 0.8426 (p) REVERT: E 352 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8601 (tm-30) REVERT: E 412 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7458 (ptt90) REVERT: E 455 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8577 (mmmm) REVERT: E 507 HIS cc_start: 0.8827 (t-90) cc_final: 0.8441 (t-90) REVERT: F 16 ASP cc_start: 0.8519 (t0) cc_final: 0.8261 (t0) REVERT: F 34 ASP cc_start: 0.9202 (t0) cc_final: 0.8954 (t0) REVERT: F 75 GLU cc_start: 0.7211 (pm20) cc_final: 0.6744 (pm20) REVERT: F 92 HIS cc_start: 0.9257 (p90) cc_final: 0.8879 (p90) REVERT: F 100 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.9077 (pt0) REVERT: F 105 ARG cc_start: 0.8327 (mtm110) cc_final: 0.8110 (ttp80) REVERT: F 108 LYS cc_start: 0.8641 (tptp) cc_final: 0.8234 (tppt) REVERT: F 179 MET cc_start: 0.7962 (pp-130) cc_final: 0.6844 (ppp) REVERT: F 198 ASN cc_start: 0.9217 (m110) cc_final: 0.8705 (m-40) REVERT: F 199 GLU cc_start: 0.8151 (pt0) cc_final: 0.7681 (tp30) REVERT: F 202 GLN cc_start: 0.8432 (pp30) cc_final: 0.7988 (pp30) REVERT: F 203 ARG cc_start: 0.8728 (tpp-160) cc_final: 0.8123 (mtp-110) REVERT: F 214 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8015 (tm-30) REVERT: F 244 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8278 (mt) REVERT: F 245 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8135 (mm) REVERT: F 286 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8833 (tmt) REVERT: F 300 ILE cc_start: 0.8529 (mm) cc_final: 0.8292 (mm) REVERT: F 319 ASP cc_start: 0.8483 (m-30) cc_final: 0.8236 (m-30) REVERT: F 352 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8608 (tm-30) REVERT: F 353 TYR cc_start: 0.9012 (t80) cc_final: 0.8796 (t80) REVERT: F 412 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7467 (ptt90) REVERT: F 420 MET cc_start: 0.6748 (mtm) cc_final: 0.6541 (mtm) REVERT: F 455 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8608 (mmmm) REVERT: F 474 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8523 (mtpt) REVERT: F 507 HIS cc_start: 0.8835 (t-90) cc_final: 0.8420 (t-90) REVERT: G 34 ASP cc_start: 0.9259 (t0) cc_final: 0.8942 (t0) REVERT: G 75 GLU cc_start: 0.7214 (pm20) cc_final: 0.6578 (mp0) REVERT: G 108 LYS cc_start: 0.8664 (tptp) cc_final: 0.8290 (tppt) REVERT: G 179 MET cc_start: 0.7717 (pp-130) cc_final: 0.6457 (ppp) REVERT: G 198 ASN cc_start: 0.9197 (m110) cc_final: 0.8736 (m-40) REVERT: G 199 GLU cc_start: 0.8161 (pt0) cc_final: 0.7778 (tp30) REVERT: G 202 GLN cc_start: 0.8485 (pp30) cc_final: 0.8143 (pp30) REVERT: G 203 ARG cc_start: 0.8835 (tpp-160) cc_final: 0.8053 (mtp-110) REVERT: G 214 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8028 (tm-30) REVERT: G 245 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8116 (mm) REVERT: G 259 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8106 (mtp180) REVERT: G 274 ASP cc_start: 0.8911 (t0) cc_final: 0.8706 (t0) REVERT: G 300 ILE cc_start: 0.8610 (mm) cc_final: 0.8347 (mm) REVERT: G 319 ASP cc_start: 0.8520 (m-30) cc_final: 0.8247 (m-30) REVERT: G 327 SER cc_start: 0.8628 (p) cc_final: 0.8376 (p) REVERT: G 352 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8541 (tm-30) REVERT: G 353 TYR cc_start: 0.8942 (t80) cc_final: 0.8735 (t80) REVERT: G 412 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7578 (ptt90) REVERT: G 455 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8600 (mmmm) REVERT: G 474 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8644 (mtpt) REVERT: G 487 GLU cc_start: 0.9013 (tt0) cc_final: 0.8642 (tt0) REVERT: G 507 HIS cc_start: 0.8811 (t-90) cc_final: 0.8387 (t-90) REVERT: H 75 GLU cc_start: 0.7106 (pm20) cc_final: 0.6590 (pm20) REVERT: H 100 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.9115 (pt0) REVERT: H 179 MET cc_start: 0.8040 (pp-130) cc_final: 0.6879 (ppp) REVERT: H 194 LEU cc_start: 0.8700 (mm) cc_final: 0.8300 (mm) REVERT: H 198 ASN cc_start: 0.9232 (m110) cc_final: 0.8699 (m-40) REVERT: H 199 GLU cc_start: 0.8126 (pt0) cc_final: 0.7787 (tp30) REVERT: H 202 GLN cc_start: 0.8500 (pp30) cc_final: 0.7975 (pp30) REVERT: H 214 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8111 (tm-30) REVERT: H 245 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8144 (mm) REVERT: H 286 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8727 (tmt) REVERT: H 319 ASP cc_start: 0.8562 (m-30) cc_final: 0.8295 (m-30) REVERT: H 412 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7506 (ptt90) REVERT: H 507 HIS cc_start: 0.8801 (t-90) cc_final: 0.8397 (t-90) outliers start: 172 outliers final: 95 residues processed: 973 average time/residue: 0.1942 time to fit residues: 307.0143 Evaluate side-chains 885 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 767 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 100 GLN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 496 SER Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 38 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 311 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 304 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 303 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 198 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103815 restraints weight = 54034.136| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.66 r_work: 0.3102 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32096 Z= 0.134 Angle : 0.703 8.342 43488 Z= 0.355 Chirality : 0.047 0.153 4968 Planarity : 0.004 0.039 5448 Dihedral : 8.323 70.149 4517 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.13 % Allowed : 21.76 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 3968 helix: -0.40 (0.14), residues: 1288 sheet: -1.48 (0.22), residues: 528 loop : -1.63 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 231 TYR 0.010 0.001 TYR F 348 PHE 0.012 0.001 PHE A 24 HIS 0.003 0.000 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (32072) covalent geometry : angle 0.70309 / 0.35 (43488) hydrogen bonds : bond 0.03127 / 2.02 ( 1009) hydrogen bonds : angle 5.10831 / 3.45 ( 2835) Misc. bond : bond 0.00069 / 0.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 904 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8897 (m-40) cc_final: 0.8573 (p0) REVERT: A 75 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: A 94 ASN cc_start: 0.9187 (t0) cc_final: 0.8923 (t0) REVERT: A 134 LYS cc_start: 0.8059 (pttp) cc_final: 0.7662 (pttm) REVERT: A 136 ARG cc_start: 0.8553 (ptm-80) cc_final: 0.8270 (ptt180) REVERT: A 179 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6452 (ppp) REVERT: A 198 ASN cc_start: 0.9263 (m-40) cc_final: 0.8673 (m-40) REVERT: A 199 GLU cc_start: 0.8166 (pt0) cc_final: 0.7802 (tp30) REVERT: A 202 GLN cc_start: 0.8594 (pp30) cc_final: 0.8181 (pp30) REVERT: A 203 ARG cc_start: 0.8816 (tpp-160) cc_final: 0.8176 (mtp-110) REVERT: A 209 LEU cc_start: 0.8168 (tt) cc_final: 0.7930 (tt) REVERT: A 214 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8204 (tm-30) REVERT: A 231 ARG cc_start: 0.8418 (mmm160) cc_final: 0.8131 (mmp80) REVERT: A 274 ASP cc_start: 0.8929 (t0) cc_final: 0.8676 (t0) REVERT: A 285 ASN cc_start: 0.8392 (m110) cc_final: 0.8126 (m110) REVERT: A 319 ASP cc_start: 0.8485 (m-30) cc_final: 0.8233 (m-30) REVERT: A 352 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8538 (tm-30) REVERT: A 353 TYR cc_start: 0.8918 (t80) cc_final: 0.8658 (t80) REVERT: A 412 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7355 (ptt90) REVERT: A 455 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8562 (mmmm) REVERT: A 474 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8660 (mtpt) REVERT: A 507 HIS cc_start: 0.8812 (t-90) cc_final: 0.8412 (t-90) REVERT: B 16 ASP cc_start: 0.8431 (t0) cc_final: 0.8158 (t0) REVERT: B 25 ASN cc_start: 0.8741 (m-40) cc_final: 0.8537 (p0) REVERT: B 75 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: B 134 LYS cc_start: 0.8081 (pttp) cc_final: 0.7609 (pttm) REVERT: B 150 MET cc_start: 0.7896 (ttt) cc_final: 0.7300 (tpp) REVERT: B 179 MET cc_start: 0.7899 (pp-130) cc_final: 0.6733 (ppp) REVERT: B 194 LEU cc_start: 0.8777 (mm) cc_final: 0.8317 (mm) REVERT: B 198 ASN cc_start: 0.9251 (m-40) cc_final: 0.8635 (m-40) REVERT: B 199 GLU cc_start: 0.8098 (pt0) cc_final: 0.7742 (tp30) REVERT: B 202 GLN cc_start: 0.8637 (pp30) cc_final: 0.8289 (pp30) REVERT: B 203 ARG cc_start: 0.8808 (tpp-160) cc_final: 0.8113 (mtp-110) REVERT: B 205 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8501 (ttmm) REVERT: B 214 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8214 (tm-30) REVERT: B 245 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 259 ARG cc_start: 0.8806 (ttm170) cc_final: 0.8597 (ttm170) REVERT: B 286 MET cc_start: 0.9217 (tpp) cc_final: 0.8978 (tpp) REVERT: B 300 ILE cc_start: 0.8679 (mm) cc_final: 0.8366 (mm) REVERT: B 319 ASP cc_start: 0.8475 (m-30) cc_final: 0.8242 (m-30) REVERT: B 352 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8573 (tm-30) REVERT: B 353 TYR cc_start: 0.8985 (t80) cc_final: 0.8720 (t80) REVERT: B 385 MET cc_start: 0.8802 (ttp) cc_final: 0.8293 (ttp) REVERT: B 412 ARG cc_start: 0.7915 (ttp80) cc_final: 0.7392 (ptt90) REVERT: B 507 HIS cc_start: 0.8783 (t-90) cc_final: 0.8383 (t-90) REVERT: C 16 ASP cc_start: 0.8451 (t0) cc_final: 0.8216 (t0) REVERT: C 75 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: C 94 ASN cc_start: 0.9189 (t0) cc_final: 0.8762 (t0) REVERT: C 100 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8982 (pt0) REVERT: C 134 LYS cc_start: 0.8122 (pttp) cc_final: 0.7688 (pttm) REVERT: C 136 ARG cc_start: 0.8579 (ptm-80) cc_final: 0.8295 (ptt180) REVERT: C 150 MET cc_start: 0.8056 (ttt) cc_final: 0.7565 (tpp) REVERT: C 174 PHE cc_start: 0.8401 (m-80) cc_final: 0.8171 (t80) REVERT: C 175 LEU cc_start: 0.8507 (mt) cc_final: 0.8124 (mt) REVERT: C 179 MET cc_start: 0.7620 (pp-130) cc_final: 0.6357 (ppp) REVERT: C 198 ASN cc_start: 0.9208 (m110) cc_final: 0.8655 (m-40) REVERT: C 199 GLU cc_start: 0.8100 (pt0) cc_final: 0.7726 (tp30) REVERT: C 202 GLN cc_start: 0.8576 (pp30) cc_final: 0.8277 (pp30) REVERT: C 203 ARG cc_start: 0.8854 (tpp-160) cc_final: 0.8189 (mtp-110) REVERT: C 205 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8481 (ttmm) REVERT: C 209 LEU cc_start: 0.8202 (tt) cc_final: 0.7995 (tt) REVERT: C 214 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8124 (tm-30) REVERT: C 231 ARG cc_start: 0.8369 (mmm160) cc_final: 0.8102 (mmp80) REVERT: C 245 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8112 (mm) REVERT: C 259 ARG cc_start: 0.8892 (ttm170) cc_final: 0.8514 (ttm170) REVERT: C 261 ASP cc_start: 0.9125 (m-30) cc_final: 0.8758 (m-30) REVERT: C 286 MET cc_start: 0.9244 (tpp) cc_final: 0.8991 (tpp) REVERT: C 319 ASP cc_start: 0.8540 (m-30) cc_final: 0.8288 (m-30) REVERT: C 352 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8588 (tm-30) REVERT: C 353 TYR cc_start: 0.8933 (t80) cc_final: 0.8674 (t80) REVERT: C 385 MET cc_start: 0.8817 (ttp) cc_final: 0.8292 (ttp) REVERT: C 412 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7401 (ptt90) REVERT: C 420 MET cc_start: 0.6581 (mtm) cc_final: 0.6344 (mtm) REVERT: C 455 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8568 (mmmm) REVERT: C 474 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8618 (mtpt) REVERT: C 496 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8892 (p) REVERT: C 507 HIS cc_start: 0.8781 (t-90) cc_final: 0.8388 (t-90) REVERT: D 16 ASP cc_start: 0.8450 (t0) cc_final: 0.8182 (t0) REVERT: D 75 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: D 134 LYS cc_start: 0.7986 (pttp) cc_final: 0.7568 (pttm) REVERT: D 136 ARG cc_start: 0.8622 (ptm-80) cc_final: 0.8354 (ptt180) REVERT: D 150 MET cc_start: 0.8084 (ttt) cc_final: 0.7444 (tpp) REVERT: D 174 PHE cc_start: 0.8139 (m-80) cc_final: 0.7542 (t80) REVERT: D 179 MET cc_start: 0.7942 (pp-130) cc_final: 0.6816 (ppp) REVERT: D 198 ASN cc_start: 0.9301 (m-40) cc_final: 0.8716 (m-40) REVERT: D 199 GLU cc_start: 0.8237 (pt0) cc_final: 0.7918 (tp30) REVERT: D 202 GLN cc_start: 0.8630 (pp30) cc_final: 0.8159 (pp30) REVERT: D 205 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8470 (ttmm) REVERT: D 214 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8104 (tm-30) REVERT: D 300 ILE cc_start: 0.8836 (mm) cc_final: 0.8565 (mm) REVERT: D 319 ASP cc_start: 0.8583 (m-30) cc_final: 0.8318 (m-30) REVERT: D 352 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8561 (tm-30) REVERT: D 353 TYR cc_start: 0.8984 (t80) cc_final: 0.8718 (t80) REVERT: D 412 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7407 (ptt90) REVERT: D 420 MET cc_start: 0.6708 (mtm) cc_final: 0.6484 (mtm) REVERT: D 455 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8590 (mmmm) REVERT: D 474 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8571 (mtpt) REVERT: D 507 HIS cc_start: 0.8790 (t-90) cc_final: 0.8367 (t-90) REVERT: E 25 ASN cc_start: 0.8853 (m-40) cc_final: 0.8590 (p0) REVERT: E 26 CYS cc_start: 0.8926 (m) cc_final: 0.8521 (t) REVERT: E 75 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: E 94 ASN cc_start: 0.9242 (t0) cc_final: 0.8805 (t0) REVERT: E 134 LYS cc_start: 0.8128 (pttp) cc_final: 0.7696 (pttm) REVERT: E 136 ARG cc_start: 0.8538 (ptm-80) cc_final: 0.8301 (ptt180) REVERT: E 150 MET cc_start: 0.7987 (ttt) cc_final: 0.7609 (tpp) REVERT: E 174 PHE cc_start: 0.8368 (m-80) cc_final: 0.7979 (t80) REVERT: E 179 MET cc_start: 0.7775 (pp-130) cc_final: 0.6544 (ppp) REVERT: E 194 LEU cc_start: 0.8712 (mm) cc_final: 0.8210 (mm) REVERT: E 198 ASN cc_start: 0.9228 (m-40) cc_final: 0.8565 (m-40) REVERT: E 199 GLU cc_start: 0.8114 (pt0) cc_final: 0.7665 (tp30) REVERT: E 202 GLN cc_start: 0.8607 (pp30) cc_final: 0.8201 (pp30) REVERT: E 203 ARG cc_start: 0.8718 (tpp-160) cc_final: 0.8056 (mtp-110) REVERT: E 209 LEU cc_start: 0.8107 (tt) cc_final: 0.7874 (tt) REVERT: E 214 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8152 (tm-30) REVERT: E 245 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8111 (mm) REVERT: E 261 ASP cc_start: 0.9106 (m-30) cc_final: 0.8695 (m-30) REVERT: E 319 ASP cc_start: 0.8531 (m-30) cc_final: 0.8275 (m-30) REVERT: E 352 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8550 (tm-30) REVERT: E 369 ASN cc_start: 0.8493 (p0) cc_final: 0.8215 (p0) REVERT: E 401 PHE cc_start: 0.8369 (p90) cc_final: 0.8168 (p90) REVERT: E 412 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7418 (ptt90) REVERT: E 418 ASP cc_start: 0.9015 (t70) cc_final: 0.8697 (t70) REVERT: E 420 MET cc_start: 0.6828 (mtm) cc_final: 0.6603 (mtm) REVERT: E 455 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8576 (mmmm) REVERT: E 474 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8502 (mmmt) REVERT: E 483 MET cc_start: 0.9398 (tmm) cc_final: 0.8903 (tmm) REVERT: E 507 HIS cc_start: 0.8808 (t-90) cc_final: 0.8437 (t-90) REVERT: F 16 ASP cc_start: 0.8437 (t0) cc_final: 0.8154 (t0) REVERT: F 25 ASN cc_start: 0.8807 (m-40) cc_final: 0.8560 (p0) REVERT: F 28 ASP cc_start: 0.8754 (t0) cc_final: 0.8317 (t0) REVERT: F 75 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: F 134 LYS cc_start: 0.8036 (pttp) cc_final: 0.7578 (pttm) REVERT: F 136 ARG cc_start: 0.8616 (ptm-80) cc_final: 0.8372 (ptt180) REVERT: F 150 MET cc_start: 0.8130 (ttt) cc_final: 0.7493 (tpp) REVERT: F 179 MET cc_start: 0.7929 (pp-130) cc_final: 0.6818 (ppp) REVERT: F 199 GLU cc_start: 0.8202 (pt0) cc_final: 0.7710 (tp30) REVERT: F 202 GLN cc_start: 0.8576 (pp30) cc_final: 0.8170 (pp30) REVERT: F 203 ARG cc_start: 0.8722 (tpp-160) cc_final: 0.8075 (mtp-110) REVERT: F 214 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8011 (tm-30) REVERT: F 300 ILE cc_start: 0.8544 (mm) cc_final: 0.8252 (mm) REVERT: F 319 ASP cc_start: 0.8471 (m-30) cc_final: 0.8255 (m-30) REVERT: F 352 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8565 (tm-30) REVERT: F 353 TYR cc_start: 0.8981 (t80) cc_final: 0.8717 (t80) REVERT: F 401 PHE cc_start: 0.8351 (p90) cc_final: 0.8147 (p90) REVERT: F 412 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7402 (ptt90) REVERT: F 420 MET cc_start: 0.6414 (mtm) cc_final: 0.6211 (mtm) REVERT: F 455 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8599 (mmmm) REVERT: F 474 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8567 (mtpt) REVERT: F 507 HIS cc_start: 0.8821 (t-90) cc_final: 0.8414 (t-90) REVERT: G 25 ASN cc_start: 0.8846 (m-40) cc_final: 0.8544 (p0) REVERT: G 34 ASP cc_start: 0.9201 (t0) cc_final: 0.8900 (t0) REVERT: G 75 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: G 94 ASN cc_start: 0.9195 (t0) cc_final: 0.8836 (t0) REVERT: G 150 MET cc_start: 0.8063 (ttt) cc_final: 0.7738 (tpp) REVERT: G 179 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6455 (ppp) REVERT: G 198 ASN cc_start: 0.9253 (m-40) cc_final: 0.8686 (m-40) REVERT: G 199 GLU cc_start: 0.8196 (pt0) cc_final: 0.7813 (tp30) REVERT: G 202 GLN cc_start: 0.8593 (pp30) cc_final: 0.8213 (pp30) REVERT: G 203 ARG cc_start: 0.8882 (tpp-160) cc_final: 0.8095 (mtp-110) REVERT: G 214 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8056 (tm-30) REVERT: G 231 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8079 (mmp80) REVERT: G 274 ASP cc_start: 0.8858 (t0) cc_final: 0.8609 (t0) REVERT: G 279 ASN cc_start: 0.8489 (t0) cc_final: 0.7991 (t0) REVERT: G 300 ILE cc_start: 0.8625 (mm) cc_final: 0.8320 (mm) REVERT: G 319 ASP cc_start: 0.8476 (m-30) cc_final: 0.8214 (m-30) REVERT: G 327 SER cc_start: 0.8476 (p) cc_final: 0.8180 (p) REVERT: G 352 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8523 (tm-30) REVERT: G 353 TYR cc_start: 0.8878 (t80) cc_final: 0.8646 (t80) REVERT: G 412 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7469 (ptt90) REVERT: G 455 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8565 (mmmm) REVERT: G 474 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8638 (mtpt) REVERT: G 507 HIS cc_start: 0.8806 (t-90) cc_final: 0.8404 (t-90) REVERT: H 25 ASN cc_start: 0.8844 (m-40) cc_final: 0.8509 (p0) REVERT: H 36 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8274 (pp) REVERT: H 75 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: H 94 ASN cc_start: 0.9186 (t0) cc_final: 0.8729 (t0) REVERT: H 132 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8523 (pp20) REVERT: H 134 LYS cc_start: 0.8033 (pttp) cc_final: 0.7667 (pttm) REVERT: H 150 MET cc_start: 0.8039 (ttt) cc_final: 0.7528 (tpp) REVERT: H 179 MET cc_start: 0.7956 (pp-130) cc_final: 0.6809 (ppp) REVERT: H 194 LEU cc_start: 0.8747 (mm) cc_final: 0.8312 (mm) REVERT: H 198 ASN cc_start: 0.9259 (m-40) cc_final: 0.8659 (m-40) REVERT: H 199 GLU cc_start: 0.8200 (pt0) cc_final: 0.7848 (tp30) REVERT: H 202 GLN cc_start: 0.8612 (pp30) cc_final: 0.8115 (pp30) REVERT: H 214 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8176 (tm-30) REVERT: H 285 ASN cc_start: 0.8686 (m110) cc_final: 0.8374 (m110) REVERT: H 286 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8745 (tmt) REVERT: H 300 ILE cc_start: 0.8715 (mm) cc_final: 0.8413 (mm) REVERT: H 319 ASP cc_start: 0.8430 (m-30) cc_final: 0.8182 (m-30) REVERT: H 335 GLU cc_start: 0.8770 (tt0) cc_final: 0.8432 (tt0) REVERT: H 369 ASN cc_start: 0.8345 (p0) cc_final: 0.8113 (p0) REVERT: H 412 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7423 (ptt90) REVERT: H 441 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: H 507 HIS cc_start: 0.8799 (t-90) cc_final: 0.8409 (t-90) outliers start: 168 outliers final: 90 residues processed: 1013 average time/residue: 0.1860 time to fit residues: 312.3165 Evaluate side-chains 960 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 845 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ARG Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 363 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 328 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 312 optimal weight: 0.0970 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 112 GLN B 230 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 230 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 112 GLN D 230 ASN E 92 HIS E 102 ASN E 230 ASN E 285 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 HIS H 112 GLN H 230 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098354 restraints weight = 54449.773| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.56 r_work: 0.3022 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 32096 Z= 0.269 Angle : 0.801 7.782 43488 Z= 0.406 Chirality : 0.051 0.150 4968 Planarity : 0.004 0.038 5448 Dihedral : 8.653 67.353 4505 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 6.54 % Allowed : 22.25 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.13), residues: 3968 helix: -0.25 (0.14), residues: 1256 sheet: -1.84 (0.19), residues: 680 loop : -1.67 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 493 TYR 0.015 0.002 TYR F 348 PHE 0.017 0.002 PHE A 24 HIS 0.002 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.27 (32072) covalent geometry : angle 0.80119 / 0.41 (43488) hydrogen bonds : bond 0.03613 / 2.35 ( 1009) hydrogen bonds : angle 5.13906 / 3.50 ( 2835) Misc. bond : bond 0.00184 / 0.12 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 791 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: A 174 PHE cc_start: 0.8282 (m-80) cc_final: 0.8079 (t80) REVERT: A 179 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.6675 (ppp) REVERT: A 198 ASN cc_start: 0.9282 (m-40) cc_final: 0.8794 (m-40) REVERT: A 199 GLU cc_start: 0.8254 (pt0) cc_final: 0.7878 (tp30) REVERT: A 202 GLN cc_start: 0.8628 (pp30) cc_final: 0.8250 (pp30) REVERT: A 203 ARG cc_start: 0.8861 (tpp-160) cc_final: 0.8216 (mtp-110) REVERT: A 209 LEU cc_start: 0.8143 (tt) cc_final: 0.7884 (tt) REVERT: A 214 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8125 (tm-30) REVERT: A 231 ARG cc_start: 0.8429 (mmm160) cc_final: 0.8185 (mmp80) REVERT: A 319 ASP cc_start: 0.8498 (m-30) cc_final: 0.8201 (m-30) REVERT: A 353 TYR cc_start: 0.9050 (t80) cc_final: 0.8831 (t80) REVERT: A 402 PHE cc_start: 0.8769 (m-80) cc_final: 0.8553 (m-80) REVERT: A 412 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7525 (ptt90) REVERT: A 455 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8546 (mmmm) REVERT: A 474 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8729 (mtpt) REVERT: A 507 HIS cc_start: 0.8775 (t-90) cc_final: 0.8382 (t-90) REVERT: B 25 ASN cc_start: 0.8886 (m-40) cc_final: 0.8634 (p0) REVERT: B 63 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8943 (t) REVERT: B 75 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: B 94 ASN cc_start: 0.9290 (t0) cc_final: 0.8784 (t0) REVERT: B 134 LYS cc_start: 0.8050 (pttp) cc_final: 0.7698 (pttm) REVERT: B 136 ARG cc_start: 0.8631 (ptm160) cc_final: 0.7957 (ptt90) REVERT: B 179 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.6994 (ppp) REVERT: B 198 ASN cc_start: 0.9320 (m-40) cc_final: 0.8722 (m-40) REVERT: B 199 GLU cc_start: 0.8294 (pt0) cc_final: 0.7984 (tp30) REVERT: B 202 GLN cc_start: 0.8675 (pp30) cc_final: 0.8226 (pp30) REVERT: B 205 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8582 (ttmm) REVERT: B 214 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8255 (tm-30) REVERT: B 319 ASP cc_start: 0.8464 (m-30) cc_final: 0.8216 (m-30) REVERT: B 353 TYR cc_start: 0.9116 (t80) cc_final: 0.8899 (t80) REVERT: B 369 ASN cc_start: 0.8531 (p0) cc_final: 0.8307 (p0) REVERT: B 385 MET cc_start: 0.9165 (ttp) cc_final: 0.8741 (ttp) REVERT: B 412 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7561 (ptt90) REVERT: B 507 HIS cc_start: 0.8792 (t-90) cc_final: 0.8377 (t-90) REVERT: C 75 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: C 94 ASN cc_start: 0.9285 (t0) cc_final: 0.8810 (t0) REVERT: C 174 PHE cc_start: 0.8332 (m-80) cc_final: 0.7999 (t80) REVERT: C 179 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.6584 (ppp) REVERT: C 198 ASN cc_start: 0.9285 (m110) cc_final: 0.8729 (m-40) REVERT: C 199 GLU cc_start: 0.8266 (pt0) cc_final: 0.7913 (tp30) REVERT: C 202 GLN cc_start: 0.8597 (pp30) cc_final: 0.8280 (pp30) REVERT: C 203 ARG cc_start: 0.8873 (tpp-160) cc_final: 0.8234 (ttp-110) REVERT: C 205 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8506 (ttmm) REVERT: C 209 LEU cc_start: 0.8192 (tt) cc_final: 0.7928 (tt) REVERT: C 214 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8151 (tm-30) REVERT: C 245 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8162 (mm) REVERT: C 261 ASP cc_start: 0.9198 (m-30) cc_final: 0.8744 (m-30) REVERT: C 279 ASN cc_start: 0.8695 (t0) cc_final: 0.8157 (t0) REVERT: C 353 TYR cc_start: 0.9048 (t80) cc_final: 0.8842 (t80) REVERT: C 385 MET cc_start: 0.9216 (ttp) cc_final: 0.8820 (ttp) REVERT: C 412 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7540 (ptt90) REVERT: C 420 MET cc_start: 0.6958 (mtm) cc_final: 0.6701 (mtm) REVERT: C 455 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: C 474 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8671 (mtpt) REVERT: C 483 MET cc_start: 0.9366 (tmm) cc_final: 0.8815 (tmm) REVERT: C 507 HIS cc_start: 0.8798 (t-90) cc_final: 0.8391 (t-90) REVERT: D 75 GLU cc_start: 0.7448 (pm20) cc_final: 0.6853 (pm20) REVERT: D 174 PHE cc_start: 0.8140 (m-80) cc_final: 0.7500 (t80) REVERT: D 179 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7011 (ppp) REVERT: D 199 GLU cc_start: 0.8275 (pt0) cc_final: 0.7867 (tp30) REVERT: D 202 GLN cc_start: 0.8671 (pp30) cc_final: 0.8032 (pp30) REVERT: D 205 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8531 (ttmm) REVERT: D 214 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8166 (tm-30) REVERT: D 259 ARG cc_start: 0.9015 (ttm170) cc_final: 0.8720 (ttm170) REVERT: D 300 ILE cc_start: 0.8843 (mm) cc_final: 0.8561 (mm) REVERT: D 353 TYR cc_start: 0.9115 (t80) cc_final: 0.8899 (t80) REVERT: D 385 MET cc_start: 0.9160 (ttp) cc_final: 0.8709 (ttp) REVERT: D 412 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7578 (ptt90) REVERT: D 420 MET cc_start: 0.6823 (mtm) cc_final: 0.6542 (mtm) REVERT: D 455 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8626 (mmmm) REVERT: D 474 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8640 (mtpt) REVERT: D 507 HIS cc_start: 0.8820 (t-90) cc_final: 0.8414 (t-90) REVERT: E 25 ASN cc_start: 0.9015 (m-40) cc_final: 0.8723 (p0) REVERT: E 75 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: E 174 PHE cc_start: 0.8335 (m-80) cc_final: 0.8034 (t80) REVERT: E 179 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.6767 (ppp) REVERT: E 198 ASN cc_start: 0.9249 (m-40) cc_final: 0.8705 (m-40) REVERT: E 199 GLU cc_start: 0.8268 (pt0) cc_final: 0.7797 (tp30) REVERT: E 202 GLN cc_start: 0.8646 (pp30) cc_final: 0.8260 (pp30) REVERT: E 203 ARG cc_start: 0.8741 (tpp-160) cc_final: 0.8078 (mtp-110) REVERT: E 214 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8075 (tm-30) REVERT: E 245 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8129 (mm) REVERT: E 261 ASP cc_start: 0.9171 (m-30) cc_final: 0.8672 (m-30) REVERT: E 385 MET cc_start: 0.8813 (ttp) cc_final: 0.8611 (ttp) REVERT: E 412 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7545 (ptt90) REVERT: E 420 MET cc_start: 0.6933 (mtm) cc_final: 0.6667 (mtm) REVERT: E 455 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8590 (mmmm) REVERT: E 474 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8560 (mtpt) REVERT: E 507 HIS cc_start: 0.8821 (t-90) cc_final: 0.8447 (t-90) REVERT: F 75 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: F 179 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.6948 (ppp) REVERT: F 198 ASN cc_start: 0.9321 (m-40) cc_final: 0.8765 (m-40) REVERT: F 199 GLU cc_start: 0.8239 (pt0) cc_final: 0.7816 (tp30) REVERT: F 202 GLN cc_start: 0.8616 (pp30) cc_final: 0.8178 (pp30) REVERT: F 203 ARG cc_start: 0.8762 (tpp-160) cc_final: 0.8119 (mtp-110) REVERT: F 214 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8075 (tm-30) REVERT: F 319 ASP cc_start: 0.8444 (m-30) cc_final: 0.8180 (m-30) REVERT: F 343 GLN cc_start: 0.9303 (tp40) cc_final: 0.9047 (tp-100) REVERT: F 353 TYR cc_start: 0.9100 (t80) cc_final: 0.8897 (t80) REVERT: F 385 MET cc_start: 0.9098 (ttp) cc_final: 0.8642 (ttp) REVERT: F 412 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7614 (ptt90) REVERT: F 420 MET cc_start: 0.6815 (mtm) cc_final: 0.6556 (mtm) REVERT: F 455 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8650 (mmmm) REVERT: F 474 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8652 (mtpt) REVERT: F 507 HIS cc_start: 0.8815 (t-90) cc_final: 0.8410 (t-90) REVERT: G 75 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: G 134 LYS cc_start: 0.8027 (pttp) cc_final: 0.7668 (pttm) REVERT: G 179 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.6633 (ppp) REVERT: G 199 GLU cc_start: 0.8315 (pt0) cc_final: 0.7992 (tp30) REVERT: G 202 GLN cc_start: 0.8613 (pp30) cc_final: 0.7867 (tm-30) REVERT: G 203 ARG cc_start: 0.8897 (tpp-160) cc_final: 0.8591 (tpp80) REVERT: G 231 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8175 (mmp80) REVERT: G 259 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7551 (mtp180) REVERT: G 279 ASN cc_start: 0.8788 (t0) cc_final: 0.8320 (t0) REVERT: G 385 MET cc_start: 0.8750 (ttp) cc_final: 0.8495 (ttp) REVERT: G 412 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7606 (ptt90) REVERT: G 455 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8547 (mmmm) REVERT: G 474 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8726 (mtpt) REVERT: G 487 GLU cc_start: 0.8913 (tt0) cc_final: 0.8310 (tt0) REVERT: G 507 HIS cc_start: 0.8812 (t-90) cc_final: 0.8416 (t-90) REVERT: H 25 ASN cc_start: 0.8930 (m-40) cc_final: 0.8615 (p0) REVERT: H 36 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8644 (pp) REVERT: H 75 GLU cc_start: 0.7333 (pm20) cc_final: 0.6671 (pm20) REVERT: H 94 ASN cc_start: 0.9242 (t0) cc_final: 0.8774 (t0) REVERT: H 132 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8500 (pp20) REVERT: H 134 LYS cc_start: 0.7971 (pttp) cc_final: 0.7580 (pttm) REVERT: H 179 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7084 (ppp) REVERT: H 198 ASN cc_start: 0.9294 (m-40) cc_final: 0.8782 (m-40) REVERT: H 199 GLU cc_start: 0.8300 (pt0) cc_final: 0.7959 (tp30) REVERT: H 202 GLN cc_start: 0.8657 (pp30) cc_final: 0.8151 (pp30) REVERT: H 214 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8128 (tm-30) REVERT: H 286 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8732 (tmt) REVERT: H 319 ASP cc_start: 0.8428 (m-30) cc_final: 0.8159 (m-30) REVERT: H 369 ASN cc_start: 0.8559 (p0) cc_final: 0.8319 (p0) REVERT: H 385 MET cc_start: 0.9065 (ttp) cc_final: 0.8588 (ttp) REVERT: H 412 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7627 (ptt90) REVERT: H 441 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: H 507 HIS cc_start: 0.8814 (t-90) cc_final: 0.8433 (t-90) outliers start: 214 outliers final: 142 residues processed: 946 average time/residue: 0.1873 time to fit residues: 290.5730 Evaluate side-chains 927 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 758 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Chi-restraints excluded: chain H residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 300 optimal weight: 0.0170 chunk 212 optimal weight: 0.4980 chunk 220 optimal weight: 0.9990 chunk 340 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 369 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN B 92 HIS B 285 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.135788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103214 restraints weight = 53525.344| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.60 r_work: 0.3098 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32096 Z= 0.136 Angle : 0.724 8.947 43488 Z= 0.363 Chirality : 0.047 0.162 4968 Planarity : 0.004 0.103 5448 Dihedral : 8.292 73.113 4505 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.65 % Allowed : 25.06 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3968 helix: -0.07 (0.15), residues: 1256 sheet: -1.00 (0.24), residues: 448 loop : -1.57 (0.14), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 126 TYR 0.011 0.001 TYR E 110 PHE 0.012 0.001 PHE H 24 HIS 0.004 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (32072) covalent geometry : angle 0.72352 / 0.36 (43488) hydrogen bonds : bond 0.03186 / 2.07 ( 1009) hydrogen bonds : angle 4.99330 / 3.38 ( 2835) Misc. bond : bond 0.00085 / 0.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 884 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8925 (m-40) cc_final: 0.8595 (p0) REVERT: A 75 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: A 94 ASN cc_start: 0.9162 (t0) cc_final: 0.8880 (t0) REVERT: A 136 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8125 (ptt180) REVERT: A 174 PHE cc_start: 0.8245 (m-80) cc_final: 0.7899 (t80) REVERT: A 179 MET cc_start: 0.7784 (pp-130) cc_final: 0.6510 (ppp) REVERT: A 198 ASN cc_start: 0.9289 (m-40) cc_final: 0.8801 (m-40) REVERT: A 199 GLU cc_start: 0.8164 (pt0) cc_final: 0.7816 (tp30) REVERT: A 202 GLN cc_start: 0.8674 (pp30) cc_final: 0.8270 (pp30) REVERT: A 203 ARG cc_start: 0.8864 (tpp-160) cc_final: 0.8195 (mtp-110) REVERT: A 209 LEU cc_start: 0.8150 (tt) cc_final: 0.7869 (tt) REVERT: A 214 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8142 (tm-30) REVERT: A 274 ASP cc_start: 0.8952 (t0) cc_final: 0.8719 (t0) REVERT: A 319 ASP cc_start: 0.8496 (m-30) cc_final: 0.8197 (m-30) REVERT: A 353 TYR cc_start: 0.8927 (t80) cc_final: 0.8687 (t80) REVERT: A 412 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7294 (ptt90) REVERT: A 455 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8522 (mmmm) REVERT: A 474 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8687 (mtpt) REVERT: A 483 MET cc_start: 0.9279 (tmm) cc_final: 0.8638 (tmm) REVERT: A 507 HIS cc_start: 0.8775 (t-90) cc_final: 0.8406 (t-90) REVERT: B 25 ASN cc_start: 0.8843 (m-40) cc_final: 0.8613 (p0) REVERT: B 75 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: B 94 ASN cc_start: 0.9232 (t0) cc_final: 0.8784 (t0) REVERT: B 134 LYS cc_start: 0.7970 (pttp) cc_final: 0.7684 (pttm) REVERT: B 179 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.6730 (ppp) REVERT: B 198 ASN cc_start: 0.9266 (m-40) cc_final: 0.8688 (m-40) REVERT: B 199 GLU cc_start: 0.8133 (pt0) cc_final: 0.7601 (tp30) REVERT: B 202 GLN cc_start: 0.8712 (pp30) cc_final: 0.8094 (pp30) REVERT: B 205 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8468 (ttmm) REVERT: B 214 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8129 (tm-30) REVERT: B 224 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7403 (ttm170) REVERT: B 245 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8109 (mm) REVERT: B 319 ASP cc_start: 0.8455 (m-30) cc_final: 0.8223 (m-30) REVERT: B 353 TYR cc_start: 0.8984 (t80) cc_final: 0.8748 (t80) REVERT: B 369 ASN cc_start: 0.8391 (p0) cc_final: 0.8156 (p0) REVERT: B 385 MET cc_start: 0.9140 (ttp) cc_final: 0.8640 (ttp) REVERT: B 412 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7364 (ptt90) REVERT: B 474 LYS cc_start: 0.8886 (mttt) cc_final: 0.8624 (mmmt) REVERT: B 483 MET cc_start: 0.9341 (tmm) cc_final: 0.8611 (tmm) REVERT: B 507 HIS cc_start: 0.8764 (t-90) cc_final: 0.8363 (t-90) REVERT: C 75 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: C 94 ASN cc_start: 0.9125 (t0) cc_final: 0.8712 (t0) REVERT: C 100 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.9076 (pt0) REVERT: C 134 LYS cc_start: 0.8014 (pttp) cc_final: 0.7765 (pttm) REVERT: C 136 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8133 (ptt180) REVERT: C 174 PHE cc_start: 0.8375 (m-80) cc_final: 0.7993 (t80) REVERT: C 179 MET cc_start: 0.7842 (pp-130) cc_final: 0.6555 (ppp) REVERT: C 198 ASN cc_start: 0.9255 (m110) cc_final: 0.8742 (m-40) REVERT: C 199 GLU cc_start: 0.8148 (pt0) cc_final: 0.7820 (tp30) REVERT: C 202 GLN cc_start: 0.8654 (pp30) cc_final: 0.8345 (pp30) REVERT: C 203 ARG cc_start: 0.8881 (tpp-160) cc_final: 0.8223 (ttp-110) REVERT: C 205 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8460 (ttmm) REVERT: C 214 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8104 (tm-30) REVERT: C 245 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8153 (mm) REVERT: C 259 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8596 (ttm170) REVERT: C 261 ASP cc_start: 0.9193 (m-30) cc_final: 0.8687 (m-30) REVERT: C 353 TYR cc_start: 0.8911 (t80) cc_final: 0.8707 (t80) REVERT: C 385 MET cc_start: 0.9015 (ttp) cc_final: 0.8496 (ttp) REVERT: C 412 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7342 (ptt90) REVERT: C 420 MET cc_start: 0.6937 (mtm) cc_final: 0.6709 (mtm) REVERT: C 455 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8549 (mmmm) REVERT: C 474 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8644 (mtpt) REVERT: C 496 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8827 (p) REVERT: C 507 HIS cc_start: 0.8839 (t-90) cc_final: 0.8458 (t-90) REVERT: D 25 ASN cc_start: 0.8841 (m-40) cc_final: 0.8508 (p0) REVERT: D 70 MET cc_start: 0.9121 (ptt) cc_final: 0.8910 (ptt) REVERT: D 75 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: D 94 ASN cc_start: 0.9211 (t0) cc_final: 0.8769 (t0) REVERT: D 136 ARG cc_start: 0.8574 (ptm-80) cc_final: 0.8140 (ptt180) REVERT: D 150 MET cc_start: 0.8010 (ttt) cc_final: 0.7269 (tpp) REVERT: D 179 MET cc_start: 0.8116 (pp-130) cc_final: 0.6972 (ppp) REVERT: D 198 ASN cc_start: 0.9304 (m-40) cc_final: 0.8817 (m-40) REVERT: D 199 GLU cc_start: 0.8227 (pt0) cc_final: 0.7867 (tp30) REVERT: D 202 GLN cc_start: 0.8731 (pp30) cc_final: 0.8169 (pp30) REVERT: D 205 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8365 (ttmm) REVERT: D 259 ARG cc_start: 0.8882 (ttm170) cc_final: 0.8632 (ttm170) REVERT: D 285 ASN cc_start: 0.8580 (m110) cc_final: 0.8313 (m110) REVERT: D 300 ILE cc_start: 0.8764 (mm) cc_final: 0.8529 (mm) REVERT: D 327 SER cc_start: 0.9023 (p) cc_final: 0.8799 (p) REVERT: D 353 TYR cc_start: 0.9018 (t80) cc_final: 0.8779 (t80) REVERT: D 379 LEU cc_start: 0.9368 (mt) cc_final: 0.9140 (mt) REVERT: D 385 MET cc_start: 0.9112 (ttp) cc_final: 0.8617 (ttp) REVERT: D 412 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7325 (ptt90) REVERT: D 420 MET cc_start: 0.6765 (mtm) cc_final: 0.6468 (mtm) REVERT: D 455 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8602 (mmmm) REVERT: D 474 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8610 (mtpt) REVERT: D 483 MET cc_start: 0.9204 (tmm) cc_final: 0.8511 (tmm) REVERT: D 507 HIS cc_start: 0.8793 (t-90) cc_final: 0.8364 (t-90) REVERT: E 25 ASN cc_start: 0.8871 (m-40) cc_final: 0.8624 (p0) REVERT: E 26 CYS cc_start: 0.9172 (m) cc_final: 0.8594 (t) REVERT: E 75 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: E 94 ASN cc_start: 0.9265 (t0) cc_final: 0.8852 (t0) REVERT: E 100 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8950 (pt0) REVERT: E 136 ARG cc_start: 0.8545 (ptm-80) cc_final: 0.8147 (ptt180) REVERT: E 174 PHE cc_start: 0.8285 (m-80) cc_final: 0.7971 (t80) REVERT: E 179 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.6651 (ppp) REVERT: E 198 ASN cc_start: 0.9241 (m-40) cc_final: 0.8687 (m-40) REVERT: E 199 GLU cc_start: 0.8115 (pt0) cc_final: 0.7681 (tp30) REVERT: E 202 GLN cc_start: 0.8666 (pp30) cc_final: 0.8258 (pp30) REVERT: E 203 ARG cc_start: 0.8756 (tpp-160) cc_final: 0.8068 (mtp-110) REVERT: E 214 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8145 (tm-30) REVERT: E 245 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8034 (mm) REVERT: E 261 ASP cc_start: 0.9187 (m-30) cc_final: 0.8634 (m-30) REVERT: E 312 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8235 (t0) REVERT: E 385 MET cc_start: 0.8819 (ttp) cc_final: 0.8590 (ttp) REVERT: E 409 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8213 (tppt) REVERT: E 412 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7378 (ptt90) REVERT: E 420 MET cc_start: 0.6914 (mtm) cc_final: 0.6620 (mtm) REVERT: E 455 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8556 (mmmm) REVERT: E 474 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8580 (mtpt) REVERT: E 507 HIS cc_start: 0.8832 (t-90) cc_final: 0.8466 (t-90) REVERT: F 25 ASN cc_start: 0.8778 (m-40) cc_final: 0.8528 (p0) REVERT: F 28 ASP cc_start: 0.8748 (t0) cc_final: 0.8414 (t0) REVERT: F 68 SER cc_start: 0.9332 (p) cc_final: 0.9114 (p) REVERT: F 75 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6689 (pm20) REVERT: F 92 HIS cc_start: 0.9078 (p90) cc_final: 0.8778 (p-80) REVERT: F 94 ASN cc_start: 0.9114 (t0) cc_final: 0.8691 (t0) REVERT: F 134 LYS cc_start: 0.8000 (pttp) cc_final: 0.7667 (pttm) REVERT: F 136 ARG cc_start: 0.8623 (ptm-80) cc_final: 0.8080 (ptt90) REVERT: F 150 MET cc_start: 0.8082 (ttt) cc_final: 0.7299 (tpp) REVERT: F 179 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.6801 (ppp) REVERT: F 198 ASN cc_start: 0.9288 (m-40) cc_final: 0.8737 (m-40) REVERT: F 199 GLU cc_start: 0.8229 (pt0) cc_final: 0.7745 (tp30) REVERT: F 202 GLN cc_start: 0.8686 (pp30) cc_final: 0.8308 (pp30) REVERT: F 203 ARG cc_start: 0.8758 (tpp-160) cc_final: 0.8071 (mtp-110) REVERT: F 214 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8141 (tm-30) REVERT: F 259 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8510 (ttm170) REVERT: F 285 ASN cc_start: 0.8548 (m110) cc_final: 0.8304 (m110) REVERT: F 353 TYR cc_start: 0.8984 (t80) cc_final: 0.8777 (t80) REVERT: F 379 LEU cc_start: 0.9488 (mt) cc_final: 0.9162 (mt) REVERT: F 385 MET cc_start: 0.9022 (ttp) cc_final: 0.8480 (ttp) REVERT: F 409 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8219 (tppt) REVERT: F 412 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7459 (ptt90) REVERT: F 420 MET cc_start: 0.6834 (mtm) cc_final: 0.6629 (mtm) REVERT: F 474 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8633 (mtpt) REVERT: F 483 MET cc_start: 0.9289 (tmm) cc_final: 0.8574 (tmm) REVERT: F 507 HIS cc_start: 0.8826 (t-90) cc_final: 0.8429 (t-90) REVERT: G 28 ASP cc_start: 0.8699 (t0) cc_final: 0.8433 (t0) REVERT: G 75 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: G 94 ASN cc_start: 0.9203 (t0) cc_final: 0.8839 (t0) REVERT: G 134 LYS cc_start: 0.7965 (pttp) cc_final: 0.7713 (pttm) REVERT: G 136 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.7987 (ptt90) REVERT: G 179 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6467 (ppp) REVERT: G 199 GLU cc_start: 0.8215 (pt0) cc_final: 0.7621 (tp30) REVERT: G 202 GLN cc_start: 0.8639 (pp30) cc_final: 0.7758 (pp30) REVERT: G 203 ARG cc_start: 0.8900 (tpp-160) cc_final: 0.8049 (mtp-110) REVERT: G 214 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8066 (tm-30) REVERT: G 231 ARG cc_start: 0.8369 (mmm160) cc_final: 0.8135 (mmp80) REVERT: G 274 ASP cc_start: 0.8964 (t0) cc_final: 0.8710 (t0) REVERT: G 279 ASN cc_start: 0.8590 (t0) cc_final: 0.8299 (t0) REVERT: G 343 GLN cc_start: 0.8704 (tp40) cc_final: 0.8490 (tp-100) REVERT: G 412 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7479 (ptt90) REVERT: G 455 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8517 (mmmm) REVERT: G 474 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8673 (mtpt) REVERT: G 483 MET cc_start: 0.9286 (tmm) cc_final: 0.8607 (tmm) REVERT: G 487 GLU cc_start: 0.8975 (tt0) cc_final: 0.8566 (tt0) REVERT: G 507 HIS cc_start: 0.8775 (t-90) cc_final: 0.8389 (t-90) REVERT: H 25 ASN cc_start: 0.8878 (m-40) cc_final: 0.8558 (p0) REVERT: H 36 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8371 (pp) REVERT: H 75 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6733 (pm20) REVERT: H 94 ASN cc_start: 0.9121 (t0) cc_final: 0.8699 (t0) REVERT: H 134 LYS cc_start: 0.7910 (pttp) cc_final: 0.7576 (pttm) REVERT: H 179 MET cc_start: 0.8120 (pp-130) cc_final: 0.6985 (ppp) REVERT: H 194 LEU cc_start: 0.8819 (mm) cc_final: 0.8357 (mm) REVERT: H 198 ASN cc_start: 0.9277 (m-40) cc_final: 0.8764 (m-40) REVERT: H 199 GLU cc_start: 0.8218 (pt0) cc_final: 0.7838 (tp30) REVERT: H 202 GLN cc_start: 0.8694 (pp30) cc_final: 0.8317 (pp30) REVERT: H 203 ARG cc_start: 0.8807 (tpp-160) cc_final: 0.8166 (mtp-110) REVERT: H 214 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8127 (tm-30) REVERT: H 230 ASN cc_start: 0.8606 (t0) cc_final: 0.8081 (t0) REVERT: H 259 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8517 (ttm170) REVERT: H 286 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8750 (tmt) REVERT: H 300 ILE cc_start: 0.8734 (mm) cc_final: 0.8513 (mm) REVERT: H 319 ASP cc_start: 0.8448 (m-30) cc_final: 0.8180 (m-30) REVERT: H 385 MET cc_start: 0.9091 (ttp) cc_final: 0.8569 (ttp) REVERT: H 409 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8154 (tppt) REVERT: H 412 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7422 (ptt90) REVERT: H 441 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: H 483 MET cc_start: 0.9225 (tmm) cc_final: 0.8529 (tmm) REVERT: H 507 HIS cc_start: 0.8817 (t-90) cc_final: 0.8443 (t-90) outliers start: 152 outliers final: 90 residues processed: 971 average time/residue: 0.1935 time to fit residues: 307.3322 Evaluate side-chains 941 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 824 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 271 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 358 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 369 optimal weight: 10.0000 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN C 21 GLN C 92 HIS ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102631 restraints weight = 53790.406| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.61 r_work: 0.3084 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32096 Z= 0.165 Angle : 0.735 8.153 43488 Z= 0.371 Chirality : 0.048 0.178 4968 Planarity : 0.004 0.088 5448 Dihedral : 8.150 73.602 4501 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.98 % Allowed : 25.79 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.14), residues: 3968 helix: -0.01 (0.15), residues: 1256 sheet: -0.91 (0.25), residues: 448 loop : -1.54 (0.14), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 231 TYR 0.011 0.001 TYR G 348 PHE 0.013 0.001 PHE H 24 HIS 0.004 0.001 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (32072) covalent geometry : angle 0.73467 / 0.37 (43488) hydrogen bonds : bond 0.03249 / 2.13 ( 1009) hydrogen bonds : angle 4.93846 / 3.36 ( 2835) Misc. bond : bond 0.00129 / 0.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 847 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8981 (m-40) cc_final: 0.8627 (p0) REVERT: A 75 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: A 94 ASN cc_start: 0.9225 (t0) cc_final: 0.8771 (t0) REVERT: A 136 ARG cc_start: 0.8572 (ptm-80) cc_final: 0.8149 (ptt180) REVERT: A 174 PHE cc_start: 0.8155 (m-80) cc_final: 0.7778 (t80) REVERT: A 179 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6538 (ppp) REVERT: A 198 ASN cc_start: 0.9324 (m-40) cc_final: 0.8804 (m-40) REVERT: A 199 GLU cc_start: 0.8212 (pt0) cc_final: 0.7846 (tp30) REVERT: A 202 GLN cc_start: 0.8712 (pp30) cc_final: 0.8296 (pp30) REVERT: A 203 ARG cc_start: 0.8882 (tpp-160) cc_final: 0.8203 (mtp-110) REVERT: A 214 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8211 (tm-30) REVERT: A 274 ASP cc_start: 0.8989 (t0) cc_final: 0.8757 (t0) REVERT: A 279 ASN cc_start: 0.8513 (t0) cc_final: 0.7745 (t0) REVERT: A 319 ASP cc_start: 0.8487 (m-30) cc_final: 0.8197 (m-30) REVERT: A 353 TYR cc_start: 0.8952 (t80) cc_final: 0.8722 (t80) REVERT: A 412 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7199 (ptt90) REVERT: A 455 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8548 (mmmm) REVERT: A 474 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8697 (mtpt) REVERT: A 507 HIS cc_start: 0.8787 (t-90) cc_final: 0.8459 (t-90) REVERT: B 25 ASN cc_start: 0.8862 (m-40) cc_final: 0.8626 (p0) REVERT: B 34 ASP cc_start: 0.9279 (t0) cc_final: 0.9076 (t0) REVERT: B 36 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8486 (pp) REVERT: B 68 SER cc_start: 0.9265 (p) cc_final: 0.9055 (p) REVERT: B 75 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: B 134 LYS cc_start: 0.7954 (pttp) cc_final: 0.7691 (pttm) REVERT: B 179 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.6920 (ppp) REVERT: B 199 GLU cc_start: 0.8140 (pt0) cc_final: 0.7507 (tp30) REVERT: B 202 GLN cc_start: 0.8736 (pp30) cc_final: 0.8216 (pp30) REVERT: B 203 ARG cc_start: 0.8858 (tpp-160) cc_final: 0.8099 (mtp-110) REVERT: B 205 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8571 (ttmm) REVERT: B 209 LEU cc_start: 0.8354 (tt) cc_final: 0.8126 (tt) REVERT: B 214 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8136 (tm-30) REVERT: B 224 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7411 (ttm170) REVERT: B 319 ASP cc_start: 0.8511 (m-30) cc_final: 0.8223 (m-30) REVERT: B 353 TYR cc_start: 0.9024 (t80) cc_final: 0.8794 (t80) REVERT: B 379 LEU cc_start: 0.9458 (mt) cc_final: 0.9228 (mt) REVERT: B 385 MET cc_start: 0.9213 (ttp) cc_final: 0.8815 (ttp) REVERT: B 412 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7368 (ptt90) REVERT: B 507 HIS cc_start: 0.8769 (t-90) cc_final: 0.8407 (t-90) REVERT: C 75 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: C 94 ASN cc_start: 0.9188 (t0) cc_final: 0.8761 (t0) REVERT: C 100 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.9070 (pt0) REVERT: C 136 ARG cc_start: 0.8575 (ptm-80) cc_final: 0.8152 (ptt180) REVERT: C 174 PHE cc_start: 0.8285 (m-80) cc_final: 0.7869 (t80) REVERT: C 179 MET cc_start: 0.7890 (pp-130) cc_final: 0.6626 (ppp) REVERT: C 198 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.8718 (m-40) REVERT: C 199 GLU cc_start: 0.8180 (pt0) cc_final: 0.7858 (tp30) REVERT: C 202 GLN cc_start: 0.8684 (pp30) cc_final: 0.8360 (pp30) REVERT: C 203 ARG cc_start: 0.8909 (tpp-160) cc_final: 0.8229 (ttp-110) REVERT: C 205 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8422 (ttmm) REVERT: C 214 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8126 (tm-30) REVERT: C 261 ASP cc_start: 0.9203 (m-30) cc_final: 0.8670 (m-30) REVERT: C 279 ASN cc_start: 0.8598 (t0) cc_final: 0.8273 (t0) REVERT: C 353 TYR cc_start: 0.8962 (t80) cc_final: 0.8753 (t80) REVERT: C 385 MET cc_start: 0.9073 (ttp) cc_final: 0.8648 (ttp) REVERT: C 412 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7340 (ptt90) REVERT: C 420 MET cc_start: 0.6987 (mtm) cc_final: 0.6741 (mtm) REVERT: C 455 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8525 (mmmm) REVERT: C 474 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8661 (mtpt) REVERT: C 496 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8828 (p) REVERT: C 507 HIS cc_start: 0.8837 (t-90) cc_final: 0.8489 (t-90) REVERT: D 25 ASN cc_start: 0.8861 (m-40) cc_final: 0.8536 (p0) REVERT: D 36 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8438 (pp) REVERT: D 75 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: D 94 ASN cc_start: 0.9185 (t0) cc_final: 0.8748 (t0) REVERT: D 136 ARG cc_start: 0.8579 (ptm-80) cc_final: 0.8153 (ptt180) REVERT: D 150 MET cc_start: 0.7892 (ttt) cc_final: 0.7233 (tpp) REVERT: D 179 MET cc_start: 0.8168 (pp-130) cc_final: 0.7015 (ppp) REVERT: D 198 ASN cc_start: 0.9342 (m-40) cc_final: 0.8826 (m-40) REVERT: D 199 GLU cc_start: 0.8263 (pt0) cc_final: 0.7894 (tp30) REVERT: D 202 GLN cc_start: 0.8768 (pp30) cc_final: 0.8197 (pp30) REVERT: D 205 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8362 (ttmm) REVERT: D 214 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8116 (tm-30) REVERT: D 259 ARG cc_start: 0.8847 (ttm170) cc_final: 0.8579 (ttm170) REVERT: D 300 ILE cc_start: 0.8801 (mm) cc_final: 0.8580 (mm) REVERT: D 353 TYR cc_start: 0.9033 (t80) cc_final: 0.8800 (t80) REVERT: D 379 LEU cc_start: 0.9430 (mt) cc_final: 0.9208 (mt) REVERT: D 385 MET cc_start: 0.9280 (ttp) cc_final: 0.8861 (ttp) REVERT: D 412 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7381 (ptt90) REVERT: D 420 MET cc_start: 0.6826 (mtm) cc_final: 0.6525 (mtm) REVERT: D 455 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8616 (mmmm) REVERT: D 474 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8626 (mtpt) REVERT: D 507 HIS cc_start: 0.8814 (t-90) cc_final: 0.8441 (t-90) REVERT: E 25 ASN cc_start: 0.8895 (m-40) cc_final: 0.8644 (p0) REVERT: E 26 CYS cc_start: 0.9190 (m) cc_final: 0.8621 (t) REVERT: E 75 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: E 136 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8153 (ptt180) REVERT: E 150 MET cc_start: 0.7906 (ttt) cc_final: 0.7557 (tpp) REVERT: E 174 PHE cc_start: 0.8194 (m-80) cc_final: 0.7838 (t80) REVERT: E 179 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6675 (ppp) REVERT: E 198 ASN cc_start: 0.9304 (m-40) cc_final: 0.8751 (m-40) REVERT: E 199 GLU cc_start: 0.8224 (pt0) cc_final: 0.7836 (tp30) REVERT: E 202 GLN cc_start: 0.8703 (pp30) cc_final: 0.8311 (pp30) REVERT: E 203 ARG cc_start: 0.8775 (tpp-160) cc_final: 0.8140 (ttp-110) REVERT: E 214 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8149 (tm-30) REVERT: E 231 ARG cc_start: 0.8331 (mmm160) cc_final: 0.8051 (mmp80) REVERT: E 245 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8078 (mm) REVERT: E 261 ASP cc_start: 0.9211 (m-30) cc_final: 0.8813 (m-30) REVERT: E 312 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8237 (t0) REVERT: E 379 LEU cc_start: 0.9523 (mt) cc_final: 0.9265 (mt) REVERT: E 385 MET cc_start: 0.8979 (ttp) cc_final: 0.8723 (ttp) REVERT: E 409 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8232 (tppt) REVERT: E 412 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7388 (ptt90) REVERT: E 420 MET cc_start: 0.6946 (mtm) cc_final: 0.6622 (mtm) REVERT: E 455 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8570 (mmmm) REVERT: E 474 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8614 (mtpt) REVERT: E 483 MET cc_start: 0.9347 (tmm) cc_final: 0.8781 (tmm) REVERT: E 507 HIS cc_start: 0.8880 (t-90) cc_final: 0.8534 (t-90) REVERT: F 75 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: F 92 HIS cc_start: 0.9117 (p90) cc_final: 0.8870 (p-80) REVERT: F 94 ASN cc_start: 0.9129 (t0) cc_final: 0.8710 (t0) REVERT: F 136 ARG cc_start: 0.8641 (ptm-80) cc_final: 0.8117 (ptt90) REVERT: F 150 MET cc_start: 0.8123 (ttt) cc_final: 0.7402 (tpp) REVERT: F 179 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.6897 (ppp) REVERT: F 199 GLU cc_start: 0.8197 (pt0) cc_final: 0.7747 (tp30) REVERT: F 202 GLN cc_start: 0.8677 (pp30) cc_final: 0.8320 (pp30) REVERT: F 203 ARG cc_start: 0.8774 (tpp-160) cc_final: 0.8154 (ttp-110) REVERT: F 214 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8090 (tm-30) REVERT: F 259 ARG cc_start: 0.8749 (ttm170) cc_final: 0.8510 (ttm170) REVERT: F 353 TYR cc_start: 0.9040 (t80) cc_final: 0.8831 (t80) REVERT: F 385 MET cc_start: 0.9128 (ttp) cc_final: 0.8680 (ttp) REVERT: F 412 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7491 (ptt90) REVERT: F 420 MET cc_start: 0.6935 (mtm) cc_final: 0.6720 (mtm) REVERT: F 474 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8654 (mtpt) REVERT: F 507 HIS cc_start: 0.8863 (t-90) cc_final: 0.8499 (t-90) REVERT: G 75 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: G 94 ASN cc_start: 0.9246 (t0) cc_final: 0.8833 (t0) REVERT: G 134 LYS cc_start: 0.7977 (pttp) cc_final: 0.7759 (pttm) REVERT: G 136 ARG cc_start: 0.8497 (ptm-80) cc_final: 0.8024 (ptt90) REVERT: G 174 PHE cc_start: 0.8247 (m-80) cc_final: 0.7915 (t80) REVERT: G 179 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6486 (ppp) REVERT: G 199 GLU cc_start: 0.8264 (pt0) cc_final: 0.7911 (tp30) REVERT: G 202 GLN cc_start: 0.8666 (pp30) cc_final: 0.8324 (tm-30) REVERT: G 203 ARG cc_start: 0.8935 (tpp-160) cc_final: 0.8230 (mtp-110) REVERT: G 214 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8088 (tm-30) REVERT: G 231 ARG cc_start: 0.8354 (mmm160) cc_final: 0.8152 (mmp80) REVERT: G 274 ASP cc_start: 0.9001 (t0) cc_final: 0.8751 (t0) REVERT: G 343 GLN cc_start: 0.8762 (tp40) cc_final: 0.8562 (tp-100) REVERT: G 412 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7437 (ptt90) REVERT: G 455 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8554 (mmmm) REVERT: G 474 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8689 (mtpt) REVERT: G 487 GLU cc_start: 0.8978 (tt0) cc_final: 0.8519 (tt0) REVERT: G 507 HIS cc_start: 0.8816 (t-90) cc_final: 0.8457 (t-90) REVERT: H 25 ASN cc_start: 0.8879 (m-40) cc_final: 0.8557 (p0) REVERT: H 75 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: H 94 ASN cc_start: 0.9195 (t0) cc_final: 0.8776 (t0) REVERT: H 134 LYS cc_start: 0.7904 (pttp) cc_final: 0.7598 (pttm) REVERT: H 179 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.6971 (ppp) REVERT: H 194 LEU cc_start: 0.8832 (mm) cc_final: 0.8383 (mm) REVERT: H 198 ASN cc_start: 0.9324 (m-40) cc_final: 0.8794 (m-40) REVERT: H 199 GLU cc_start: 0.8269 (pt0) cc_final: 0.7868 (tp30) REVERT: H 202 GLN cc_start: 0.8711 (pp30) cc_final: 0.8321 (pp30) REVERT: H 203 ARG cc_start: 0.8815 (tpp-160) cc_final: 0.8168 (mtp-110) REVERT: H 214 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8154 (tm-30) REVERT: H 259 ARG cc_start: 0.8862 (ttm170) cc_final: 0.8641 (ttm170) REVERT: H 319 ASP cc_start: 0.8426 (m-30) cc_final: 0.8186 (m-30) REVERT: H 379 LEU cc_start: 0.9452 (mt) cc_final: 0.9224 (mt) REVERT: H 385 MET cc_start: 0.9203 (ttp) cc_final: 0.8800 (ttp) REVERT: H 412 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7435 (ptt90) REVERT: H 441 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: H 507 HIS cc_start: 0.8816 (t-90) cc_final: 0.8468 (t-90) outliers start: 163 outliers final: 105 residues processed: 937 average time/residue: 0.1873 time to fit residues: 288.0343 Evaluate side-chains 937 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 805 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 293 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 188 optimal weight: 0.3980 chunk 324 optimal weight: 0.0000 chunk 219 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102545 restraints weight = 53582.600| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.61 r_work: 0.3100 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32096 Z= 0.156 Angle : 0.734 8.861 43488 Z= 0.370 Chirality : 0.048 0.172 4968 Planarity : 0.004 0.098 5448 Dihedral : 8.092 74.924 4501 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.34 % Allowed : 27.14 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3968 helix: -0.10 (0.15), residues: 1280 sheet: -1.52 (0.24), residues: 488 loop : -1.25 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 231 TYR 0.011 0.001 TYR C 289 PHE 0.011 0.001 PHE B 24 HIS 0.004 0.001 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (32072) covalent geometry : angle 0.73384 / 0.37 (43488) hydrogen bonds : bond 0.03171 / 2.07 ( 1009) hydrogen bonds : angle 4.91534 / 3.34 ( 2835) Misc. bond : bond 0.00118 / 0.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 850 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8952 (m-40) cc_final: 0.8618 (p0) REVERT: A 75 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: A 94 ASN cc_start: 0.9286 (t0) cc_final: 0.8810 (t0) REVERT: A 136 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.8145 (ptt180) REVERT: A 174 PHE cc_start: 0.8183 (m-80) cc_final: 0.7819 (t80) REVERT: A 179 MET cc_start: 0.7868 (pp-130) cc_final: 0.6674 (ppp) REVERT: A 198 ASN cc_start: 0.9328 (m-40) cc_final: 0.8773 (m-40) REVERT: A 199 GLU cc_start: 0.8169 (pt0) cc_final: 0.7818 (tp30) REVERT: A 202 GLN cc_start: 0.8719 (pp30) cc_final: 0.8301 (pp30) REVERT: A 203 ARG cc_start: 0.8822 (tpp-160) cc_final: 0.8115 (mtp-110) REVERT: A 214 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8331 (tm-30) REVERT: A 274 ASP cc_start: 0.9004 (t0) cc_final: 0.8745 (t0) REVERT: A 277 GLN cc_start: 0.8659 (tp40) cc_final: 0.8425 (tm-30) REVERT: A 279 ASN cc_start: 0.8792 (t0) cc_final: 0.7585 (t0) REVERT: A 353 TYR cc_start: 0.8925 (t80) cc_final: 0.8697 (t80) REVERT: A 412 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7140 (ptt90) REVERT: A 455 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8538 (mmmm) REVERT: A 474 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8687 (mtpt) REVERT: A 483 MET cc_start: 0.9269 (tmm) cc_final: 0.8577 (tmm) REVERT: A 507 HIS cc_start: 0.8777 (t-90) cc_final: 0.8456 (t-90) REVERT: B 25 ASN cc_start: 0.8836 (m-40) cc_final: 0.8613 (p0) REVERT: B 36 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8461 (pp) REVERT: B 75 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: B 134 LYS cc_start: 0.7941 (pttp) cc_final: 0.7706 (pttm) REVERT: B 179 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.6875 (ppp) REVERT: B 199 GLU cc_start: 0.8121 (pt0) cc_final: 0.7396 (tp30) REVERT: B 202 GLN cc_start: 0.8719 (pp30) cc_final: 0.8157 (pp30) REVERT: B 203 ARG cc_start: 0.8868 (tpp-160) cc_final: 0.8091 (mtp-110) REVERT: B 205 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8583 (ttmm) REVERT: B 209 LEU cc_start: 0.8390 (tt) cc_final: 0.8176 (tt) REVERT: B 214 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8135 (tm-30) REVERT: B 224 ARG cc_start: 0.8314 (tpp80) cc_final: 0.7404 (ttm170) REVERT: B 300 ILE cc_start: 0.8699 (mm) cc_final: 0.8463 (mm) REVERT: B 319 ASP cc_start: 0.8565 (m-30) cc_final: 0.8317 (m-30) REVERT: B 353 TYR cc_start: 0.8981 (t80) cc_final: 0.8736 (t80) REVERT: B 385 MET cc_start: 0.9214 (ttp) cc_final: 0.8787 (ttp) REVERT: B 412 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7196 (ptt90) REVERT: B 483 MET cc_start: 0.9281 (tmm) cc_final: 0.8521 (tmm) REVERT: B 507 HIS cc_start: 0.8778 (t-90) cc_final: 0.8423 (t-90) REVERT: C 75 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: C 94 ASN cc_start: 0.9195 (t0) cc_final: 0.8757 (t0) REVERT: C 136 ARG cc_start: 0.8570 (ptm-80) cc_final: 0.8167 (ptt180) REVERT: C 179 MET cc_start: 0.7850 (pp-130) cc_final: 0.6567 (ppp) REVERT: C 198 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.8752 (m-40) REVERT: C 199 GLU cc_start: 0.8227 (pt0) cc_final: 0.7901 (tp30) REVERT: C 202 GLN cc_start: 0.8735 (pp30) cc_final: 0.8396 (pp30) REVERT: C 203 ARG cc_start: 0.8929 (tpp-160) cc_final: 0.8258 (ttp-110) REVERT: C 205 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8487 (ttmm) REVERT: C 214 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8121 (tm-30) REVERT: C 245 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8145 (mm) REVERT: C 261 ASP cc_start: 0.9195 (m-30) cc_final: 0.8849 (m-30) REVERT: C 385 MET cc_start: 0.9054 (ttp) cc_final: 0.8639 (ttp) REVERT: C 412 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7300 (ptt90) REVERT: C 455 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8542 (mmmm) REVERT: C 474 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8657 (mtpt) REVERT: C 483 MET cc_start: 0.9371 (tmm) cc_final: 0.8880 (tmm) REVERT: C 496 SER cc_start: 0.9178 (OUTLIER) cc_final: 0.8904 (p) REVERT: C 507 HIS cc_start: 0.8857 (t-90) cc_final: 0.8515 (t-90) REVERT: D 36 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8463 (pp) REVERT: D 75 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: D 94 ASN cc_start: 0.9158 (t0) cc_final: 0.8719 (t0) REVERT: D 136 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8136 (ptt180) REVERT: D 150 MET cc_start: 0.7828 (ttt) cc_final: 0.7225 (tpp) REVERT: D 179 MET cc_start: 0.8152 (pp-130) cc_final: 0.7006 (ppp) REVERT: D 199 GLU cc_start: 0.8255 (pt0) cc_final: 0.7879 (tp30) REVERT: D 202 GLN cc_start: 0.8761 (pp30) cc_final: 0.8182 (pp30) REVERT: D 205 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8332 (ttmm) REVERT: D 214 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8151 (tm-30) REVERT: D 300 ILE cc_start: 0.8824 (mm) cc_final: 0.8624 (mm) REVERT: D 353 TYR cc_start: 0.8998 (t80) cc_final: 0.8751 (t80) REVERT: D 385 MET cc_start: 0.9277 (ttp) cc_final: 0.8864 (ttp) REVERT: D 412 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7271 (ptt90) REVERT: D 420 MET cc_start: 0.6846 (mtm) cc_final: 0.6533 (mtm) REVERT: D 455 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8622 (mmmm) REVERT: D 474 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8590 (mtpt) REVERT: D 483 MET cc_start: 0.9200 (tmm) cc_final: 0.8481 (tmm) REVERT: D 507 HIS cc_start: 0.8819 (t-90) cc_final: 0.8446 (t-90) REVERT: E 25 ASN cc_start: 0.8886 (m-40) cc_final: 0.8643 (p0) REVERT: E 26 CYS cc_start: 0.9180 (m) cc_final: 0.8632 (t) REVERT: E 75 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: E 94 ASN cc_start: 0.9270 (t0) cc_final: 0.8841 (t0) REVERT: E 136 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8272 (ptt180) REVERT: E 150 MET cc_start: 0.7887 (ttt) cc_final: 0.7565 (tpp) REVERT: E 174 PHE cc_start: 0.8181 (m-80) cc_final: 0.7847 (t80) REVERT: E 179 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.6849 (ppp) REVERT: E 198 ASN cc_start: 0.9305 (m-40) cc_final: 0.8752 (m-40) REVERT: E 199 GLU cc_start: 0.8136 (pt0) cc_final: 0.7831 (tp30) REVERT: E 202 GLN cc_start: 0.8701 (pp30) cc_final: 0.8310 (pp30) REVERT: E 203 ARG cc_start: 0.8778 (tpp-160) cc_final: 0.8105 (ttp-110) REVERT: E 214 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8214 (tm-30) REVERT: E 231 ARG cc_start: 0.8323 (mmm160) cc_final: 0.8073 (mmp80) REVERT: E 245 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8123 (mm) REVERT: E 261 ASP cc_start: 0.9213 (m-30) cc_final: 0.8797 (m-30) REVERT: E 312 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8213 (t0) REVERT: E 319 ASP cc_start: 0.8593 (m-30) cc_final: 0.8255 (m-30) REVERT: E 369 ASN cc_start: 0.8496 (p0) cc_final: 0.8193 (p0) REVERT: E 385 MET cc_start: 0.8838 (ttp) cc_final: 0.8626 (ttp) REVERT: E 409 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8288 (tppt) REVERT: E 412 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7260 (ptt90) REVERT: E 420 MET cc_start: 0.6969 (mtm) cc_final: 0.6636 (mtm) REVERT: E 455 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8558 (mmmm) REVERT: E 474 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8703 (mtpt) REVERT: E 507 HIS cc_start: 0.8841 (t-90) cc_final: 0.8492 (t-90) REVERT: F 28 ASP cc_start: 0.8722 (t0) cc_final: 0.8495 (t0) REVERT: F 75 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: F 92 HIS cc_start: 0.9109 (p90) cc_final: 0.8856 (p-80) REVERT: F 94 ASN cc_start: 0.9110 (t0) cc_final: 0.8694 (t0) REVERT: F 136 ARG cc_start: 0.8630 (ptm-80) cc_final: 0.8161 (ptt90) REVERT: F 150 MET cc_start: 0.8121 (ttt) cc_final: 0.7375 (tpp) REVERT: F 179 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.6724 (ppp) REVERT: F 199 GLU cc_start: 0.8198 (pt0) cc_final: 0.7756 (tp30) REVERT: F 202 GLN cc_start: 0.8689 (pp30) cc_final: 0.8314 (pp30) REVERT: F 203 ARG cc_start: 0.8776 (tpp-160) cc_final: 0.8146 (ttp-110) REVERT: F 214 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8041 (tm-30) REVERT: F 231 ARG cc_start: 0.8315 (mmm160) cc_final: 0.7964 (mmm160) REVERT: F 259 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8441 (ttm170) REVERT: F 300 ILE cc_start: 0.8611 (mm) cc_final: 0.8353 (mm) REVERT: F 319 ASP cc_start: 0.8560 (m-30) cc_final: 0.8274 (m-30) REVERT: F 379 LEU cc_start: 0.9483 (mt) cc_final: 0.9152 (mt) REVERT: F 385 MET cc_start: 0.9133 (ttp) cc_final: 0.8672 (ttp) REVERT: F 409 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8134 (tppt) REVERT: F 412 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7412 (ptt90) REVERT: F 420 MET cc_start: 0.6932 (mtm) cc_final: 0.6697 (mtm) REVERT: F 474 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8650 (mtpt) REVERT: F 483 MET cc_start: 0.9187 (tmm) cc_final: 0.8440 (tmm) REVERT: F 507 HIS cc_start: 0.8813 (t-90) cc_final: 0.8438 (t-90) REVERT: G 75 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: G 94 ASN cc_start: 0.9224 (t0) cc_final: 0.8783 (t0) REVERT: G 136 ARG cc_start: 0.8491 (ptm-80) cc_final: 0.7856 (ptt90) REVERT: G 174 PHE cc_start: 0.8194 (m-80) cc_final: 0.7796 (t80) REVERT: G 179 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.6480 (ppp) REVERT: G 198 ASN cc_start: 0.9310 (m-40) cc_final: 0.8786 (m-40) REVERT: G 199 GLU cc_start: 0.8130 (pt0) cc_final: 0.7765 (tp30) REVERT: G 202 GLN cc_start: 0.8650 (pp30) cc_final: 0.8273 (pp30) REVERT: G 203 ARG cc_start: 0.8916 (tpp-160) cc_final: 0.8147 (mtp-110) REVERT: G 231 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8170 (mmp80) REVERT: G 259 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7831 (mtp180) REVERT: G 274 ASP cc_start: 0.9007 (t0) cc_final: 0.8782 (t0) REVERT: G 379 LEU cc_start: 0.9513 (mt) cc_final: 0.9175 (mt) REVERT: G 412 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7351 (ptt90) REVERT: G 455 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8526 (mmmm) REVERT: G 474 LYS cc_start: 0.8904 (mtpt) cc_final: 0.8678 (mtpt) REVERT: G 483 MET cc_start: 0.9218 (tmm) cc_final: 0.8505 (tmm) REVERT: G 487 GLU cc_start: 0.8989 (tt0) cc_final: 0.8539 (tt0) REVERT: G 507 HIS cc_start: 0.8784 (t-90) cc_final: 0.8455 (t-90) REVERT: H 25 ASN cc_start: 0.8864 (m-40) cc_final: 0.8556 (p0) REVERT: H 75 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6766 (pm20) REVERT: H 94 ASN cc_start: 0.9206 (t0) cc_final: 0.8807 (t0) REVERT: H 134 LYS cc_start: 0.7911 (pttp) cc_final: 0.7684 (pttm) REVERT: H 136 ARG cc_start: 0.8537 (ptm-80) cc_final: 0.8042 (ptt180) REVERT: H 150 MET cc_start: 0.7926 (ttt) cc_final: 0.7257 (tpp) REVERT: H 179 MET cc_start: 0.8116 (pp-130) cc_final: 0.6947 (ppp) REVERT: H 194 LEU cc_start: 0.8842 (mm) cc_final: 0.8401 (mm) REVERT: H 198 ASN cc_start: 0.9341 (m-40) cc_final: 0.8810 (m-40) REVERT: H 199 GLU cc_start: 0.8277 (pt0) cc_final: 0.7876 (tp30) REVERT: H 202 GLN cc_start: 0.8733 (pp30) cc_final: 0.8336 (pp30) REVERT: H 203 ARG cc_start: 0.8815 (tpp-160) cc_final: 0.8141 (mtp-110) REVERT: H 214 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8192 (tm-30) REVERT: H 232 ASP cc_start: 0.8583 (t70) cc_final: 0.8195 (t70) REVERT: H 385 MET cc_start: 0.9160 (ttp) cc_final: 0.8689 (ttp) REVERT: H 412 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7336 (ptt90) REVERT: H 441 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: H 483 MET cc_start: 0.9220 (tmm) cc_final: 0.8466 (tmm) REVERT: H 507 HIS cc_start: 0.8805 (t-90) cc_final: 0.8459 (t-90) outliers start: 142 outliers final: 95 residues processed: 920 average time/residue: 0.1856 time to fit residues: 282.1706 Evaluate side-chains 934 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 814 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 155 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 383 optimal weight: 0.2980 chunk 172 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 213 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN B 92 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.136913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104201 restraints weight = 53592.740| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.67 r_work: 0.3116 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32096 Z= 0.142 Angle : 0.730 9.372 43488 Z= 0.367 Chirality : 0.048 0.202 4968 Planarity : 0.004 0.087 5448 Dihedral : 8.026 77.140 4501 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.94 % Allowed : 28.73 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3968 helix: 0.00 (0.15), residues: 1256 sheet: -1.34 (0.23), residues: 528 loop : -1.37 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 231 TYR 0.016 0.001 TYR B 233 PHE 0.010 0.001 PHE B 24 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (32072) covalent geometry : angle 0.73029 / 0.37 (43488) hydrogen bonds : bond 0.03130 / 2.06 ( 1009) hydrogen bonds : angle 4.87803 / 3.31 ( 2835) Misc. bond : bond 0.00110 / 0.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 848 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8887 (m-40) cc_final: 0.8617 (p0) REVERT: A 75 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: A 94 ASN cc_start: 0.9292 (t0) cc_final: 0.8824 (t0) REVERT: A 136 ARG cc_start: 0.8577 (ptm-80) cc_final: 0.8021 (ptt90) REVERT: A 174 PHE cc_start: 0.8205 (m-80) cc_final: 0.7871 (t80) REVERT: A 179 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.6545 (ppp) REVERT: A 198 ASN cc_start: 0.9320 (m-40) cc_final: 0.8772 (m-40) REVERT: A 199 GLU cc_start: 0.8177 (pt0) cc_final: 0.7605 (tp30) REVERT: A 202 GLN cc_start: 0.8757 (pp30) cc_final: 0.8044 (pp30) REVERT: A 203 ARG cc_start: 0.8839 (tpp-160) cc_final: 0.8038 (mtp-110) REVERT: A 214 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8322 (tm-30) REVERT: A 279 ASN cc_start: 0.8818 (t0) cc_final: 0.7775 (t0) REVERT: A 353 TYR cc_start: 0.8910 (t80) cc_final: 0.8691 (t80) REVERT: A 395 GLU cc_start: 0.8448 (pm20) cc_final: 0.8051 (pm20) REVERT: A 412 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7066 (ptt90) REVERT: A 455 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8546 (mmmm) REVERT: A 474 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8641 (mtpt) REVERT: A 483 MET cc_start: 0.9263 (tmm) cc_final: 0.8629 (tmm) REVERT: A 507 HIS cc_start: 0.8750 (t-90) cc_final: 0.8409 (t-90) REVERT: B 25 ASN cc_start: 0.8799 (m-40) cc_final: 0.8589 (p0) REVERT: B 36 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8351 (pp) REVERT: B 75 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: B 179 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6724 (ppp) REVERT: B 199 GLU cc_start: 0.8117 (pt0) cc_final: 0.7382 (tp30) REVERT: B 202 GLN cc_start: 0.8718 (pp30) cc_final: 0.8151 (pp30) REVERT: B 203 ARG cc_start: 0.8831 (tpp-160) cc_final: 0.7961 (mtp-110) REVERT: B 205 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8557 (ttmm) REVERT: B 214 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8147 (tm-30) REVERT: B 224 ARG cc_start: 0.8318 (tpp80) cc_final: 0.7393 (ttm170) REVERT: B 300 ILE cc_start: 0.8743 (mm) cc_final: 0.8479 (mm) REVERT: B 353 TYR cc_start: 0.8951 (t80) cc_final: 0.8733 (t80) REVERT: B 385 MET cc_start: 0.9187 (ttp) cc_final: 0.8781 (ttp) REVERT: B 412 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7355 (ptt90) REVERT: B 483 MET cc_start: 0.9255 (tmm) cc_final: 0.8538 (tmm) REVERT: B 507 HIS cc_start: 0.8772 (t-90) cc_final: 0.8415 (t-90) REVERT: C 75 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: C 94 ASN cc_start: 0.9192 (t0) cc_final: 0.8765 (t0) REVERT: C 136 ARG cc_start: 0.8574 (ptm-80) cc_final: 0.8286 (ptt180) REVERT: C 174 PHE cc_start: 0.8284 (m-80) cc_final: 0.7921 (t80) REVERT: C 179 MET cc_start: 0.7733 (pp-130) cc_final: 0.6687 (pp-130) REVERT: C 198 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.8728 (m-40) REVERT: C 199 GLU cc_start: 0.8125 (pt0) cc_final: 0.7568 (tp30) REVERT: C 202 GLN cc_start: 0.8717 (pp30) cc_final: 0.8073 (pp30) REVERT: C 203 ARG cc_start: 0.8928 (tpp-160) cc_final: 0.8103 (mtp180) REVERT: C 205 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8471 (ttmm) REVERT: C 214 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8127 (tm-30) REVERT: C 231 ARG cc_start: 0.8348 (mmm160) cc_final: 0.8064 (mmp80) REVERT: C 245 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8207 (mm) REVERT: C 261 ASP cc_start: 0.9175 (m-30) cc_final: 0.8827 (m-30) REVERT: C 385 MET cc_start: 0.9035 (ttp) cc_final: 0.8627 (ttp) REVERT: C 395 GLU cc_start: 0.8344 (pm20) cc_final: 0.7923 (pm20) REVERT: C 412 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7307 (ptt90) REVERT: C 455 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8557 (mmmm) REVERT: C 474 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8649 (mtpt) REVERT: C 483 MET cc_start: 0.9396 (tmm) cc_final: 0.8894 (tmm) REVERT: C 496 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8865 (p) REVERT: C 507 HIS cc_start: 0.8834 (t-90) cc_final: 0.8494 (t-90) REVERT: D 36 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8371 (pp) REVERT: D 75 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6841 (pm20) REVERT: D 94 ASN cc_start: 0.9217 (t0) cc_final: 0.8758 (t0) REVERT: D 136 ARG cc_start: 0.8589 (ptm-80) cc_final: 0.8312 (ptt180) REVERT: D 150 MET cc_start: 0.7814 (ttt) cc_final: 0.7228 (tpp) REVERT: D 179 MET cc_start: 0.8127 (pp-130) cc_final: 0.6970 (ppp) REVERT: D 198 ASN cc_start: 0.9332 (m-40) cc_final: 0.8780 (m-40) REVERT: D 199 GLU cc_start: 0.8143 (pt0) cc_final: 0.7776 (tp30) REVERT: D 202 GLN cc_start: 0.8743 (pp30) cc_final: 0.8364 (pp30) REVERT: D 203 ARG cc_start: 0.8872 (tpp-160) cc_final: 0.8121 (mtp-110) REVERT: D 205 LYS cc_start: 0.9022 (mtpp) cc_final: 0.8413 (ttmm) REVERT: D 214 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8151 (tm-30) REVERT: D 353 TYR cc_start: 0.8953 (t80) cc_final: 0.8733 (t80) REVERT: D 385 MET cc_start: 0.9253 (ttp) cc_final: 0.8834 (ttp) REVERT: D 395 GLU cc_start: 0.8406 (pm20) cc_final: 0.8054 (pm20) REVERT: D 412 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7210 (ptt90) REVERT: D 420 MET cc_start: 0.6858 (mtm) cc_final: 0.6538 (mtm) REVERT: D 455 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8651 (mmmm) REVERT: D 474 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8583 (mtpt) REVERT: D 483 MET cc_start: 0.9214 (tmm) cc_final: 0.8526 (tmm) REVERT: D 507 HIS cc_start: 0.8806 (t-90) cc_final: 0.8419 (t-90) REVERT: E 25 ASN cc_start: 0.8881 (m-40) cc_final: 0.8657 (p0) REVERT: E 26 CYS cc_start: 0.9190 (m) cc_final: 0.8650 (t) REVERT: E 75 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: E 94 ASN cc_start: 0.9268 (t0) cc_final: 0.8792 (t0) REVERT: E 136 ARG cc_start: 0.8565 (ptm-80) cc_final: 0.8317 (ptt180) REVERT: E 150 MET cc_start: 0.7869 (ttt) cc_final: 0.7569 (tpp) REVERT: E 174 PHE cc_start: 0.8182 (m-80) cc_final: 0.7854 (t80) REVERT: E 179 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.6884 (ppp) REVERT: E 194 LEU cc_start: 0.8720 (mm) cc_final: 0.8248 (mm) REVERT: E 198 ASN cc_start: 0.9299 (m-40) cc_final: 0.8749 (m-40) REVERT: E 199 GLU cc_start: 0.8164 (pt0) cc_final: 0.7736 (tp30) REVERT: E 202 GLN cc_start: 0.8737 (pp30) cc_final: 0.8307 (pp30) REVERT: E 203 ARG cc_start: 0.8828 (tpp-160) cc_final: 0.8022 (mtp-110) REVERT: E 214 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8235 (tm-30) REVERT: E 231 ARG cc_start: 0.8317 (mmm160) cc_final: 0.8001 (mmp80) REVERT: E 245 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8215 (mm) REVERT: E 261 ASP cc_start: 0.9219 (m-30) cc_final: 0.8812 (m-30) REVERT: E 312 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8170 (t0) REVERT: E 319 ASP cc_start: 0.8576 (m-30) cc_final: 0.8278 (m-30) REVERT: E 369 ASN cc_start: 0.8493 (p0) cc_final: 0.8188 (p0) REVERT: E 412 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7264 (ptt90) REVERT: E 420 MET cc_start: 0.6902 (mtm) cc_final: 0.6507 (mtm) REVERT: E 455 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8558 (mmmm) REVERT: E 474 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8707 (mtpt) REVERT: E 483 MET cc_start: 0.9240 (tmm) cc_final: 0.8463 (tmm) REVERT: E 507 HIS cc_start: 0.8793 (t-90) cc_final: 0.8447 (t-90) REVERT: F 25 ASN cc_start: 0.8820 (m-40) cc_final: 0.8539 (p0) REVERT: F 70 MET cc_start: 0.9167 (ptt) cc_final: 0.8897 (ptt) REVERT: F 75 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: F 92 HIS cc_start: 0.9070 (p90) cc_final: 0.8818 (p-80) REVERT: F 94 ASN cc_start: 0.9098 (t0) cc_final: 0.8710 (t0) REVERT: F 136 ARG cc_start: 0.8638 (ptm-80) cc_final: 0.8177 (ptt90) REVERT: F 150 MET cc_start: 0.8122 (ttt) cc_final: 0.7502 (tpp) REVERT: F 179 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6737 (ppp) REVERT: F 198 ASN cc_start: 0.9303 (m-40) cc_final: 0.8812 (m-40) REVERT: F 199 GLU cc_start: 0.8087 (pt0) cc_final: 0.7578 (tp30) REVERT: F 202 GLN cc_start: 0.8698 (pp30) cc_final: 0.8276 (pp30) REVERT: F 203 ARG cc_start: 0.8752 (tpp-160) cc_final: 0.8035 (mtp-110) REVERT: F 214 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8125 (tm-30) REVERT: F 231 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7936 (mmm160) REVERT: F 300 ILE cc_start: 0.8619 (mm) cc_final: 0.8383 (mm) REVERT: F 319 ASP cc_start: 0.8572 (m-30) cc_final: 0.8294 (m-30) REVERT: F 379 LEU cc_start: 0.9465 (mt) cc_final: 0.9136 (mt) REVERT: F 385 MET cc_start: 0.9107 (ttp) cc_final: 0.8682 (ttp) REVERT: F 412 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7399 (ptt90) REVERT: F 474 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8620 (mtpt) REVERT: F 483 MET cc_start: 0.9199 (tmm) cc_final: 0.8477 (tmm) REVERT: F 507 HIS cc_start: 0.8837 (t-90) cc_final: 0.8482 (t-90) REVERT: G 75 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: G 94 ASN cc_start: 0.9140 (t0) cc_final: 0.8698 (t0) REVERT: G 134 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7444 (pttm) REVERT: G 136 ARG cc_start: 0.8456 (ptm-80) cc_final: 0.8009 (ptt90) REVERT: G 174 PHE cc_start: 0.8224 (m-80) cc_final: 0.7804 (t80) REVERT: G 179 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6470 (ppp) REVERT: G 198 ASN cc_start: 0.9297 (m-40) cc_final: 0.8806 (m-40) REVERT: G 199 GLU cc_start: 0.8158 (pt0) cc_final: 0.7780 (tp30) REVERT: G 202 GLN cc_start: 0.8691 (pp30) cc_final: 0.8304 (pp30) REVERT: G 203 ARG cc_start: 0.8924 (tpp-160) cc_final: 0.8150 (mtp-110) REVERT: G 214 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8163 (tm-30) REVERT: G 259 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7877 (mtp180) REVERT: G 379 LEU cc_start: 0.9495 (mt) cc_final: 0.9166 (mt) REVERT: G 395 GLU cc_start: 0.8380 (pm20) cc_final: 0.7988 (pm20) REVERT: G 412 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7233 (ptt90) REVERT: G 448 GLN cc_start: 0.8361 (pt0) cc_final: 0.8153 (pt0) REVERT: G 455 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8530 (mmmm) REVERT: G 474 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8677 (mtpt) REVERT: G 483 MET cc_start: 0.9238 (tmm) cc_final: 0.8563 (tmm) REVERT: G 507 HIS cc_start: 0.8792 (t-90) cc_final: 0.8426 (t-90) REVERT: H 25 ASN cc_start: 0.8833 (m-40) cc_final: 0.8518 (p0) REVERT: H 75 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6978 (pm20) REVERT: H 94 ASN cc_start: 0.9214 (t0) cc_final: 0.8786 (t0) REVERT: H 136 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8084 (ptt180) REVERT: H 150 MET cc_start: 0.7958 (ttt) cc_final: 0.7350 (tpp) REVERT: H 179 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.6909 (ppp) REVERT: H 198 ASN cc_start: 0.9332 (m-40) cc_final: 0.8804 (m-40) REVERT: H 199 GLU cc_start: 0.8291 (pt0) cc_final: 0.7595 (tp30) REVERT: H 202 GLN cc_start: 0.8742 (pp30) cc_final: 0.8020 (pp30) REVERT: H 203 ARG cc_start: 0.8796 (tpp-160) cc_final: 0.8008 (mtp-110) REVERT: H 214 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8256 (tm-30) REVERT: H 232 ASP cc_start: 0.8642 (t70) cc_final: 0.8256 (t70) REVERT: H 385 MET cc_start: 0.9175 (ttp) cc_final: 0.8756 (ttp) REVERT: H 412 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7266 (ptt90) REVERT: H 441 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: H 483 MET cc_start: 0.9232 (tmm) cc_final: 0.8522 (tmm) REVERT: H 507 HIS cc_start: 0.8798 (t-90) cc_final: 0.8436 (t-90) outliers start: 129 outliers final: 88 residues processed: 902 average time/residue: 0.1784 time to fit residues: 267.0081 Evaluate side-chains 914 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 798 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 312 ASN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 380 optimal weight: 1.9990 chunk 384 optimal weight: 0.9980 chunk 269 optimal weight: 0.4980 chunk 201 optimal weight: 1.9990 chunk 378 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 387 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 368 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 213 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104473 restraints weight = 53908.573| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.70 r_work: 0.3124 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32096 Z= 0.141 Angle : 0.738 9.227 43488 Z= 0.371 Chirality : 0.048 0.244 4968 Planarity : 0.004 0.075 5448 Dihedral : 7.969 77.305 4500 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.79 % Allowed : 29.55 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3968 helix: -0.09 (0.14), residues: 1280 sheet: -1.15 (0.22), residues: 544 loop : -1.33 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 231 TYR 0.017 0.001 TYR B 233 PHE 0.009 0.001 PHE B 24 HIS 0.004 0.000 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (32072) covalent geometry : angle 0.73805 / 0.37 (43488) hydrogen bonds : bond 0.03123 / 2.05 ( 1009) hydrogen bonds : angle 4.91029 / 3.33 ( 2835) Misc. bond : bond 0.00111 / 0.07 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 804 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8864 (m-40) cc_final: 0.8610 (p0) REVERT: A 75 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6875 (pm20) REVERT: A 94 ASN cc_start: 0.9173 (t0) cc_final: 0.8714 (t0) REVERT: A 136 ARG cc_start: 0.8572 (ptm-80) cc_final: 0.8026 (ptt90) REVERT: A 174 PHE cc_start: 0.8211 (m-80) cc_final: 0.7872 (t80) REVERT: A 179 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6486 (ppp) REVERT: A 198 ASN cc_start: 0.9317 (m-40) cc_final: 0.8773 (m-40) REVERT: A 199 GLU cc_start: 0.8126 (pt0) cc_final: 0.7554 (tp30) REVERT: A 202 GLN cc_start: 0.8742 (pp30) cc_final: 0.8033 (pp30) REVERT: A 203 ARG cc_start: 0.8867 (tpp-160) cc_final: 0.8009 (mtp-110) REVERT: A 214 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8360 (tm-30) REVERT: A 231 ARG cc_start: 0.8406 (mmm160) cc_final: 0.8196 (mmp80) REVERT: A 279 ASN cc_start: 0.8840 (t0) cc_final: 0.7848 (t0) REVERT: A 312 ASN cc_start: 0.8895 (t0) cc_final: 0.8603 (t0) REVERT: A 353 TYR cc_start: 0.8890 (t80) cc_final: 0.8674 (t80) REVERT: A 395 GLU cc_start: 0.8409 (pm20) cc_final: 0.8023 (pm20) REVERT: A 412 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7056 (ptt90) REVERT: A 455 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8549 (mmmm) REVERT: A 474 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8659 (mtpt) REVERT: A 483 MET cc_start: 0.9263 (tmm) cc_final: 0.8636 (tmm) REVERT: A 507 HIS cc_start: 0.8776 (t-90) cc_final: 0.8445 (t-90) REVERT: B 36 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8335 (pp) REVERT: B 75 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: B 179 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.6679 (ppp) REVERT: B 199 GLU cc_start: 0.8118 (pt0) cc_final: 0.7385 (tp30) REVERT: B 202 GLN cc_start: 0.8735 (pp30) cc_final: 0.8170 (pp30) REVERT: B 203 ARG cc_start: 0.8837 (tpp-160) cc_final: 0.7961 (mtp-110) REVERT: B 205 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8560 (ttmm) REVERT: B 214 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8226 (tm-30) REVERT: B 224 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7372 (ttm170) REVERT: B 300 ILE cc_start: 0.8747 (mm) cc_final: 0.8490 (mm) REVERT: B 353 TYR cc_start: 0.8920 (t80) cc_final: 0.8711 (t80) REVERT: B 385 MET cc_start: 0.9217 (ttp) cc_final: 0.8830 (ttp) REVERT: B 412 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7302 (ptt90) REVERT: B 483 MET cc_start: 0.9266 (tmm) cc_final: 0.8548 (tmm) REVERT: B 507 HIS cc_start: 0.8775 (t-90) cc_final: 0.8401 (t-90) REVERT: C 75 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6864 (pm20) REVERT: C 94 ASN cc_start: 0.9203 (t0) cc_final: 0.8751 (t0) REVERT: C 136 ARG cc_start: 0.8564 (ptm-80) cc_final: 0.8277 (ptt180) REVERT: C 198 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.8735 (m-40) REVERT: C 199 GLU cc_start: 0.8150 (pt0) cc_final: 0.7596 (tp30) REVERT: C 202 GLN cc_start: 0.8723 (pp30) cc_final: 0.8073 (pp30) REVERT: C 203 ARG cc_start: 0.8933 (tpp-160) cc_final: 0.8112 (mtp180) REVERT: C 205 LYS cc_start: 0.9033 (mtpp) cc_final: 0.8448 (ttmm) REVERT: C 214 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8215 (tm-30) REVERT: C 231 ARG cc_start: 0.8365 (mmm160) cc_final: 0.8097 (mmp80) REVERT: C 245 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8262 (mm) REVERT: C 261 ASP cc_start: 0.9208 (m-30) cc_final: 0.8860 (m-30) REVERT: C 283 GLN cc_start: 0.8872 (mt0) cc_final: 0.8568 (tt0) REVERT: C 385 MET cc_start: 0.9016 (ttp) cc_final: 0.8606 (ttp) REVERT: C 412 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7263 (ptt90) REVERT: C 455 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8559 (mmmm) REVERT: C 474 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8645 (mtpt) REVERT: C 496 SER cc_start: 0.9162 (OUTLIER) cc_final: 0.8850 (p) REVERT: C 507 HIS cc_start: 0.8832 (t-90) cc_final: 0.8494 (t-90) REVERT: D 36 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8375 (pp) REVERT: D 75 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: D 136 ARG cc_start: 0.8590 (ptm-80) cc_final: 0.8107 (ptt90) REVERT: D 150 MET cc_start: 0.7932 (ttt) cc_final: 0.7302 (tpp) REVERT: D 179 MET cc_start: 0.8053 (pp-130) cc_final: 0.6892 (ppp) REVERT: D 198 ASN cc_start: 0.9334 (m-40) cc_final: 0.8799 (m-40) REVERT: D 199 GLU cc_start: 0.8200 (pt0) cc_final: 0.7651 (tp30) REVERT: D 202 GLN cc_start: 0.8802 (pp30) cc_final: 0.8038 (pp30) REVERT: D 205 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8405 (ttmm) REVERT: D 214 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8201 (tm-30) REVERT: D 353 TYR cc_start: 0.8930 (t80) cc_final: 0.8718 (t80) REVERT: D 385 MET cc_start: 0.9234 (ttp) cc_final: 0.8813 (ttp) REVERT: D 412 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7174 (ptt90) REVERT: D 420 MET cc_start: 0.6853 (mtm) cc_final: 0.6538 (mtm) REVERT: D 455 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8644 (mmmm) REVERT: D 474 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8582 (mtpt) REVERT: D 483 MET cc_start: 0.9210 (tmm) cc_final: 0.8546 (tmm) REVERT: D 507 HIS cc_start: 0.8815 (t-90) cc_final: 0.8439 (t-90) REVERT: E 25 ASN cc_start: 0.8882 (m-40) cc_final: 0.8656 (p0) REVERT: E 26 CYS cc_start: 0.9189 (m) cc_final: 0.8641 (t) REVERT: E 75 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6792 (pm20) REVERT: E 94 ASN cc_start: 0.9257 (t0) cc_final: 0.8766 (t0) REVERT: E 136 ARG cc_start: 0.8555 (ptm-80) cc_final: 0.8306 (ptt180) REVERT: E 150 MET cc_start: 0.7914 (ttt) cc_final: 0.7631 (tpp) REVERT: E 174 PHE cc_start: 0.8186 (m-80) cc_final: 0.7862 (t80) REVERT: E 179 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6904 (ppp) REVERT: E 194 LEU cc_start: 0.8748 (mm) cc_final: 0.8268 (mm) REVERT: E 198 ASN cc_start: 0.9298 (m-40) cc_final: 0.8734 (m-40) REVERT: E 199 GLU cc_start: 0.8133 (pt0) cc_final: 0.7712 (tp30) REVERT: E 202 GLN cc_start: 0.8726 (pp30) cc_final: 0.8294 (pp30) REVERT: E 203 ARG cc_start: 0.8818 (tpp-160) cc_final: 0.8015 (mtp-110) REVERT: E 214 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8320 (tm-30) REVERT: E 231 ARG cc_start: 0.8325 (mmm160) cc_final: 0.8017 (mmp80) REVERT: E 245 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8265 (mm) REVERT: E 261 ASP cc_start: 0.9203 (m-30) cc_final: 0.8800 (m-30) REVERT: E 369 ASN cc_start: 0.8510 (p0) cc_final: 0.8199 (p0) REVERT: E 412 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7297 (ptt90) REVERT: E 420 MET cc_start: 0.6923 (mtm) cc_final: 0.6520 (mtm) REVERT: E 455 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8567 (mmmm) REVERT: E 483 MET cc_start: 0.9248 (tmm) cc_final: 0.8537 (tmm) REVERT: E 507 HIS cc_start: 0.8747 (t-90) cc_final: 0.8415 (t-90) REVERT: F 25 ASN cc_start: 0.8803 (m-40) cc_final: 0.8541 (p0) REVERT: F 75 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: F 92 HIS cc_start: 0.9089 (p90) cc_final: 0.8818 (p-80) REVERT: F 94 ASN cc_start: 0.9142 (t0) cc_final: 0.8897 (t0) REVERT: F 134 LYS cc_start: 0.7793 (pttp) cc_final: 0.7550 (pttm) REVERT: F 136 ARG cc_start: 0.8646 (ptm-80) cc_final: 0.8196 (ptt90) REVERT: F 150 MET cc_start: 0.8039 (ttt) cc_final: 0.7492 (tpp) REVERT: F 179 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.6685 (ppp) REVERT: F 198 ASN cc_start: 0.9291 (m-40) cc_final: 0.8794 (m-40) REVERT: F 199 GLU cc_start: 0.8055 (pt0) cc_final: 0.7357 (tp30) REVERT: F 202 GLN cc_start: 0.8720 (pp30) cc_final: 0.8011 (pp30) REVERT: F 203 ARG cc_start: 0.8818 (tpp-160) cc_final: 0.7977 (mtp-110) REVERT: F 214 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8198 (tm-30) REVERT: F 300 ILE cc_start: 0.8620 (mm) cc_final: 0.8358 (mm) REVERT: F 379 LEU cc_start: 0.9459 (mt) cc_final: 0.9136 (mt) REVERT: F 385 MET cc_start: 0.9097 (ttp) cc_final: 0.8679 (ttp) REVERT: F 412 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7391 (ptt90) REVERT: F 474 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8610 (mtpt) REVERT: F 483 MET cc_start: 0.9192 (tmm) cc_final: 0.8479 (tmm) REVERT: F 507 HIS cc_start: 0.8830 (t-90) cc_final: 0.8475 (t-90) REVERT: G 25 ASN cc_start: 0.8842 (m-40) cc_final: 0.8528 (p0) REVERT: G 75 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: G 94 ASN cc_start: 0.9132 (t0) cc_final: 0.8677 (t0) REVERT: G 134 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7484 (pttm) REVERT: G 136 ARG cc_start: 0.8481 (ptm-80) cc_final: 0.8056 (ptt90) REVERT: G 174 PHE cc_start: 0.8163 (m-80) cc_final: 0.7686 (t80) REVERT: G 179 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6465 (ppp) REVERT: G 198 ASN cc_start: 0.9294 (m-40) cc_final: 0.8795 (m-40) REVERT: G 199 GLU cc_start: 0.8114 (pt0) cc_final: 0.7842 (tp30) REVERT: G 202 GLN cc_start: 0.8653 (pp30) cc_final: 0.8312 (pp30) REVERT: G 203 ARG cc_start: 0.8947 (tpp-160) cc_final: 0.8216 (ttp-110) REVERT: G 214 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8116 (tm-30) REVERT: G 232 ASP cc_start: 0.8625 (t70) cc_final: 0.8384 (t70) REVERT: G 319 ASP cc_start: 0.8527 (m-30) cc_final: 0.8193 (m-30) REVERT: G 379 LEU cc_start: 0.9491 (mt) cc_final: 0.9183 (mt) REVERT: G 412 ARG cc_start: 0.7589 (ttp80) cc_final: 0.7220 (ptt90) REVERT: G 455 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8545 (mmmm) REVERT: G 474 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8677 (mtpt) REVERT: G 483 MET cc_start: 0.9230 (tmm) cc_final: 0.8555 (tmm) REVERT: G 507 HIS cc_start: 0.8794 (t-90) cc_final: 0.8448 (t-90) REVERT: H 25 ASN cc_start: 0.8824 (m-40) cc_final: 0.8523 (p0) REVERT: H 75 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: H 94 ASN cc_start: 0.9231 (t0) cc_final: 0.8802 (t0) REVERT: H 136 ARG cc_start: 0.8549 (ptm-80) cc_final: 0.8083 (ptt180) REVERT: H 150 MET cc_start: 0.7939 (ttt) cc_final: 0.7355 (tpp) REVERT: H 179 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.6889 (ppp) REVERT: H 198 ASN cc_start: 0.9288 (m-40) cc_final: 0.8763 (m-40) REVERT: H 199 GLU cc_start: 0.8113 (pt0) cc_final: 0.7452 (tp30) REVERT: H 202 GLN cc_start: 0.8728 (pp30) cc_final: 0.7988 (pp30) REVERT: H 203 ARG cc_start: 0.8782 (tpp-160) cc_final: 0.7993 (mtp-110) REVERT: H 214 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8234 (tm-30) REVERT: H 385 MET cc_start: 0.9150 (ttp) cc_final: 0.8737 (ttp) REVERT: H 412 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7248 (ptt90) REVERT: H 483 MET cc_start: 0.9240 (tmm) cc_final: 0.8532 (tmm) REVERT: H 507 HIS cc_start: 0.8752 (t-90) cc_final: 0.8434 (t-90) outliers start: 124 outliers final: 83 residues processed: 858 average time/residue: 0.1789 time to fit residues: 255.0276 Evaluate side-chains 882 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 773 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 496 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 236 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 346 optimal weight: 0.6980 chunk 326 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN B 21 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN E 213 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.104985 restraints weight = 53709.388| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.66 r_work: 0.3126 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 32096 Z= 0.171 Angle : 0.831 59.139 43488 Z= 0.439 Chirality : 0.048 0.271 4968 Planarity : 0.004 0.076 5448 Dihedral : 7.964 77.249 4500 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.79 % Allowed : 29.49 % Favored : 66.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3968 helix: -0.09 (0.14), residues: 1280 sheet: -1.16 (0.22), residues: 544 loop : -1.34 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 231 TYR 0.014 0.001 TYR D 294 PHE 0.015 0.001 PHE A 131 HIS 0.004 0.000 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (32072) covalent geometry : angle 0.83149 / 0.44 (43488) hydrogen bonds : bond 0.03130 / 2.05 ( 1009) hydrogen bonds : angle 4.90849 / 3.33 ( 2835) Misc. bond : bond 0.00109 / 0.07 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7641.92 seconds wall clock time: 132 minutes 7.30 seconds (7927.30 seconds total)