Starting phenix.real_space_refine on Sat Jun 6 11:54:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7m_41986/06_2026/8u7m_41986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7m_41986/06_2026/8u7m_41986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7m_41986/06_2026/8u7m_41986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7m_41986/06_2026/8u7m_41986.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7m_41986/06_2026/8u7m_41986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7m_41986/06_2026/8u7m_41986.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 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 96 5.49 5 S 176 5.16 5 C 17576 2.51 5 N 4832 2.21 5 O 5656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28336 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "B" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "C" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "D" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "E" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "F" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "H" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 7.04, per 1000 atoms: 0.25 Number of scatterers: 28336 At special positions: 0 Unit cell: (170.52, 170.52, 105.56, 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 96 15.00 O 5656 8.00 N 4832 7.00 C 17576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6512 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 40 sheets defined 46.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 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 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.562A pdb=" N THR A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.521A pdb=" N GLU A 177 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.667A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.687A pdb=" N GLN A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 4.109A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.000A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 25 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 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.555A pdb=" N THR B 173 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.549A pdb=" N GLU B 177 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 223 through 233 removed outlier: 4.248A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.687A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.726A pdb=" N GLN B 292 " --> pdb=" O HIS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 4.104A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.000A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 486 removed outlier: 3.648A pdb=" N ARG B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'C' and resid 19 through 25 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 Processing helix chain 'C' and resid 96 through 110 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.553A pdb=" N THR C 173 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.541A pdb=" N GLU C 177 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 185 Processing helix chain 'C' and resid 193 through 203 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.730A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.712A pdb=" N GLN C 292 " --> pdb=" O HIS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 removed outlier: 4.134A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.002A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 380 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 19 through 25 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 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.556A pdb=" N GLU D 177 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 185 Processing helix chain 'D' and resid 193 through 203 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.685A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.727A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 316 removed outlier: 4.141A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.022A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 380 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.601A pdb=" N ARG D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'E' and resid 19 through 25 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 Processing helix chain 'E' and resid 96 through 110 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 169 through 173 removed outlier: 3.559A pdb=" N THR E 173 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.543A pdb=" N GLU E 177 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 185 Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.671A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.689A pdb=" N GLN E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 316 removed outlier: 4.109A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.003A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 380 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 486 removed outlier: 3.558A pdb=" N ARG E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'F' and resid 19 through 25 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 Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 169 through 173 removed outlier: 3.559A pdb=" N THR F 173 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 3.545A pdb=" N GLU F 177 " --> pdb=" O LEU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 Processing helix chain 'F' and resid 193 through 203 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.686A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.730A pdb=" N GLN F 292 " --> pdb=" O HIS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 316 removed outlier: 4.085A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.002A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 380 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'G' and resid 19 through 25 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 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 164 Processing helix chain 'G' and resid 169 through 173 removed outlier: 3.559A pdb=" N THR G 173 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.547A pdb=" N GLU G 177 " --> pdb=" O LEU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 193 through 203 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.725A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.711A pdb=" N GLN G 292 " --> pdb=" O HIS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 316 removed outlier: 4.119A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.018A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 380 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 486 removed outlier: 3.601A pdb=" N ARG G 480 " --> pdb=" O LEU G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'H' and resid 19 through 25 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 Processing helix chain 'H' and resid 96 through 110 Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 169 through 173 removed outlier: 3.558A pdb=" N THR H 173 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 178 removed outlier: 3.551A pdb=" N GLU H 177 " --> pdb=" O LEU H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 185 Processing helix chain 'H' and resid 193 through 203 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.687A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.728A pdb=" N GLN H 292 " --> pdb=" O HIS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 316 removed outlier: 4.139A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.021A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 380 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 486 removed outlier: 3.615A pdb=" N ARG H 480 " --> pdb=" O LEU H 476 " (cutoff:3.500A) 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 56 removed outlier: 6.503A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.603A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.952A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 5.980A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 222 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.493A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.194A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 144 removed outlier: 3.955A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 189 removed outlier: 5.978A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 222 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.228A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG C 322 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.965A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189 removed outlier: 5.955A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 222 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.495A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.611A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.952A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 188 through 189 removed outlier: 5.971A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 222 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.502A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.598A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 142 through 144 removed outlier: 3.959A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.566A pdb=" N ILE E 222 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.724A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 142 through 144 removed outlier: 3.960A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 188 through 189 removed outlier: 5.975A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 222 " --> pdb=" O LEU F 209 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AD5, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.243A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 142 through 144 removed outlier: 3.956A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 208 through 210 removed outlier: 3.523A pdb=" N ILE G 222 " --> pdb=" O LEU G 209 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.495A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.241A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 142 through 144 removed outlier: 3.957A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 189 removed outlier: 5.895A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE H 222 " --> pdb=" O LEU H 209 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3114 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: 5.31 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4680 1.31 - 1.43: 6900 1.43 - 1.56: 16753 1.56 - 1.69: 171 1.69 - 1.81: 296 Bond restraints: 28800 Sorted by residual: bond pdb=" C2 IMP F 604 " pdb=" N3 IMP F 604 " ideal model delta sigma weight residual 1.301 1.463 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C2 IMP E 604 " pdb=" N3 IMP E 604 " ideal model delta sigma weight residual 1.301 1.462 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C2 IMP B 604 " pdb=" N3 IMP B 604 " ideal model delta sigma weight residual 1.301 1.462 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C2 IMP C 604 " pdb=" N3 IMP C 604 " ideal model delta sigma weight residual 1.301 1.462 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C2 IMP D 604 " pdb=" N3 IMP D 604 " ideal model delta sigma weight residual 1.301 1.462 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 28795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 38566 3.87 - 7.74: 419 7.74 - 11.62: 155 11.62 - 15.49: 20 15.49 - 19.36: 16 Bond angle restraints: 39176 Sorted by residual: angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 122.69 17.18 1.00e+00 1.00e+00 2.95e+02 angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 122.81 17.06 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.82e+02 ... (remaining 39171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.74: 16652 29.74 - 59.48: 929 59.48 - 89.23: 134 89.23 - 118.97: 29 118.97 - 148.71: 32 Dihedral angle restraints: 17776 sinusoidal: 7616 harmonic: 10160 Sorted by residual: dihedral pdb=" C8 GTP B 602 " pdb=" C1' GTP B 602 " pdb=" N9 GTP B 602 " pdb=" O4' GTP B 602 " ideal model delta sinusoidal sigma weight residual 104.59 -44.12 148.71 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C8 GTP A 602 " pdb=" C1' GTP A 602 " pdb=" N9 GTP A 602 " pdb=" O4' GTP A 602 " ideal model delta sinusoidal sigma weight residual 104.59 -43.42 148.01 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" C8 GTP F 602 " pdb=" C1' GTP F 602 " pdb=" N9 GTP F 602 " pdb=" O4' GTP F 602 " ideal model delta sinusoidal sigma weight residual 104.59 -41.67 146.26 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 17773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4568 0.340 - 0.680: 24 0.680 - 1.019: 0 1.019 - 1.359: 0 1.359 - 1.699: 8 Chirality restraints: 4600 Sorted by residual: chirality pdb=" C2' ATP A 603 " pdb=" C1' ATP A 603 " pdb=" C3' ATP A 603 " pdb=" O2' ATP A 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.21e+01 chirality pdb=" C2' ATP B 603 " pdb=" C1' ATP B 603 " pdb=" C3' ATP B 603 " pdb=" O2' ATP B 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.19e+01 chirality pdb=" C2' ATP C 603 " pdb=" C1' ATP C 603 " pdb=" C3' ATP C 603 " pdb=" O2' ATP C 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.19e+01 ... (remaining 4597 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 63 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 64 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " -0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO C 64 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 63 " 0.063 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO E 64 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " 0.052 5.00e-02 4.00e+02 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2973 2.74 - 3.28: 29351 3.28 - 3.82: 46133 3.82 - 4.36: 57269 4.36 - 4.90: 98535 Nonbonded interactions: 234261 Sorted by model distance: nonbonded pdb=" NZ LYS A 205 " pdb=" OG1 THR E 180 " model vdw 2.203 3.120 nonbonded pdb=" OG1 THR D 180 " pdb=" NZ LYS F 205 " model vdw 2.206 3.120 nonbonded pdb=" OG SER B 275 " pdb=" NE2 GLN B 283 " model vdw 2.209 3.120 nonbonded pdb=" OG SER F 275 " pdb=" NE2 GLN F 283 " model vdw 2.209 3.120 nonbonded pdb=" OG SER G 275 " pdb=" NE2 GLN G 283 " model vdw 2.211 3.120 ... (remaining 234256 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 5.510 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.520 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.162 28800 Z= 0.355 Angle : 1.181 19.362 39176 Z= 0.577 Chirality : 0.089 1.699 4600 Planarity : 0.006 0.104 4800 Dihedral : 20.036 148.711 11264 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.27 % Allowed : 14.96 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3528 helix: 0.12 (0.14), residues: 1344 sheet: -0.50 (0.29), residues: 280 loop : -1.42 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 182 TYR 0.013 0.001 TYR E 459 PHE 0.013 0.002 PHE G 456 HIS 0.003 0.001 HIS D 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.35 (28800) covalent geometry : angle 1.18081 / 0.58 (39176) hydrogen bonds : bond 0.14852 / 10.33 ( 1110) hydrogen bonds : angle 6.90590 / 4.85 ( 3114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 505 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 507 average time/residue: 0.1579 time to fit residues: 132.3826 Evaluate side-chains 425 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.0370 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 372 HIS B 334 GLN B 372 HIS C 334 GLN C 372 HIS D 334 GLN D 368 GLN D 372 HIS E 334 GLN E 372 HIS F 334 GLN F 372 HIS G 334 GLN G 372 HIS H 334 GLN H 372 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.198292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.171405 restraints weight = 32668.588| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 1.83 r_work: 0.4236 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28800 Z= 0.118 Angle : 0.642 7.419 39176 Z= 0.317 Chirality : 0.045 0.181 4600 Planarity : 0.005 0.063 4800 Dihedral : 20.577 146.428 4928 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.88 % Allowed : 15.51 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3528 helix: 0.38 (0.14), residues: 1400 sheet: -0.56 (0.32), residues: 240 loop : -0.98 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 182 TYR 0.014 0.001 TYR E 289 PHE 0.018 0.002 PHE A 456 HIS 0.005 0.001 HIS D 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (28800) covalent geometry : angle 0.64159 / 0.32 (39176) hydrogen bonds : bond 0.03614 / 2.46 ( 1110) hydrogen bonds : angle 5.51904 / 3.87 ( 3114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 485 time to evaluate : 1.055 Fit side-chains REVERT: A 105 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5646 (mpt-90) REVERT: A 182 ARG cc_start: 0.5668 (ttt-90) cc_final: 0.5297 (ttt-90) REVERT: A 353 TYR cc_start: 0.7154 (t80) cc_final: 0.6805 (t80) REVERT: A 450 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7098 (ttpt) REVERT: B 105 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5690 (mpt-90) REVERT: B 179 MET cc_start: 0.7536 (ptt) cc_final: 0.7094 (ptt) REVERT: B 450 LYS cc_start: 0.7733 (ttmm) cc_final: 0.7143 (ttpt) REVERT: C 105 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.5652 (mpt-90) REVERT: C 179 MET cc_start: 0.7548 (ptt) cc_final: 0.7083 (ptt) REVERT: C 450 LYS cc_start: 0.7700 (ttmm) cc_final: 0.7070 (ttpt) REVERT: D 105 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5754 (mpt-90) REVERT: D 179 MET cc_start: 0.7556 (ptt) cc_final: 0.7077 (ptt) REVERT: D 182 ARG cc_start: 0.5714 (ttt-90) cc_final: 0.5264 (ttt-90) REVERT: D 353 TYR cc_start: 0.7170 (t80) cc_final: 0.6812 (t80) REVERT: D 450 LYS cc_start: 0.7629 (ttmm) cc_final: 0.7004 (ttpt) REVERT: E 105 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5744 (mpt-90) REVERT: E 179 MET cc_start: 0.7526 (ptt) cc_final: 0.7059 (ptt) REVERT: E 286 MET cc_start: 0.7946 (tpp) cc_final: 0.7739 (tpt) REVERT: E 353 TYR cc_start: 0.7181 (t80) cc_final: 0.6826 (t80) REVERT: E 450 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7081 (ttpt) REVERT: F 105 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.5628 (mpt-90) REVERT: F 179 MET cc_start: 0.7474 (ptt) cc_final: 0.7044 (ptt) REVERT: F 353 TYR cc_start: 0.7187 (t80) cc_final: 0.6841 (t80) REVERT: F 450 LYS cc_start: 0.7713 (ttmm) cc_final: 0.7074 (ttpt) REVERT: G 105 ARG cc_start: 0.5884 (OUTLIER) cc_final: 0.5629 (mpt-90) REVERT: G 179 MET cc_start: 0.7513 (ptt) cc_final: 0.7073 (ptt) REVERT: G 450 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7136 (ttpt) REVERT: H 105 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5777 (mpt-90) REVERT: H 179 MET cc_start: 0.7477 (ptt) cc_final: 0.7011 (ptt) REVERT: H 353 TYR cc_start: 0.7187 (t80) cc_final: 0.6828 (t80) outliers start: 55 outliers final: 23 residues processed: 521 average time/residue: 0.1623 time to fit residues: 139.2076 Evaluate side-chains 466 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 435 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 310 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 105 optimal weight: 5.9990 chunk 166 optimal weight: 0.0770 chunk 263 optimal weight: 0.8980 chunk 358 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN E 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.196471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.169777 restraints weight = 32627.510| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.84 r_work: 0.4221 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 28800 Z= 0.135 Angle : 0.610 7.247 39176 Z= 0.303 Chirality : 0.045 0.175 4600 Planarity : 0.004 0.049 4800 Dihedral : 19.214 149.456 4928 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.21 % Allowed : 15.47 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3528 helix: 0.69 (0.14), residues: 1344 sheet: -0.90 (0.31), residues: 224 loop : -0.84 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.018 0.002 TYR E 459 PHE 0.010 0.002 PHE F 24 HIS 0.002 0.001 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (28800) covalent geometry : angle 0.60964 / 0.30 (39176) hydrogen bonds : bond 0.03666 / 2.46 ( 1110) hydrogen bonds : angle 5.37848 / 3.78 ( 3114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 449 time to evaluate : 1.089 Fit side-chains REVERT: A 208 LYS cc_start: 0.4472 (mmmt) cc_final: 0.3770 (mttm) REVERT: A 283 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.5681 (tt0) REVERT: A 353 TYR cc_start: 0.7259 (t80) cc_final: 0.7044 (t80) REVERT: A 450 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7313 (ttpt) REVERT: A 459 TYR cc_start: 0.6639 (t80) cc_final: 0.6341 (t80) REVERT: A 461 ILE cc_start: 0.5398 (mp) cc_final: 0.5136 (mm) REVERT: B 179 MET cc_start: 0.7469 (ptt) cc_final: 0.7010 (ptt) REVERT: B 208 LYS cc_start: 0.4587 (mmmt) cc_final: 0.3919 (mttm) REVERT: B 456 PHE cc_start: 0.8181 (t80) cc_final: 0.7560 (t80) REVERT: B 459 TYR cc_start: 0.6851 (t80) cc_final: 0.6600 (t80) REVERT: C 179 MET cc_start: 0.7472 (ptt) cc_final: 0.7031 (ptt) REVERT: C 182 ARG cc_start: 0.5895 (ttt-90) cc_final: 0.5672 (tmt-80) REVERT: C 208 LYS cc_start: 0.4744 (mmmt) cc_final: 0.4058 (mttm) REVERT: C 450 LYS cc_start: 0.7787 (ttmm) cc_final: 0.7420 (ttpt) REVERT: C 459 TYR cc_start: 0.6577 (t80) cc_final: 0.6358 (t80) REVERT: D 179 MET cc_start: 0.7626 (ptt) cc_final: 0.7150 (ptt) REVERT: D 208 LYS cc_start: 0.4609 (mmmt) cc_final: 0.3983 (mttm) REVERT: D 353 TYR cc_start: 0.7236 (t80) cc_final: 0.7029 (t80) REVERT: D 456 PHE cc_start: 0.8168 (t80) cc_final: 0.7547 (t80) REVERT: D 459 TYR cc_start: 0.6805 (t80) cc_final: 0.6569 (t80) REVERT: E 179 MET cc_start: 0.7521 (ptt) cc_final: 0.7090 (ptt) REVERT: E 208 LYS cc_start: 0.4421 (mmmt) cc_final: 0.3769 (mttm) REVERT: E 353 TYR cc_start: 0.7257 (t80) cc_final: 0.7050 (t80) REVERT: E 450 LYS cc_start: 0.7743 (ttmm) cc_final: 0.7352 (ttpt) REVERT: E 459 TYR cc_start: 0.6674 (t80) cc_final: 0.6383 (t80) REVERT: E 461 ILE cc_start: 0.5370 (mp) cc_final: 0.5127 (mm) REVERT: F 179 MET cc_start: 0.7483 (ptt) cc_final: 0.7074 (ptt) REVERT: F 182 ARG cc_start: 0.5903 (ttt-90) cc_final: 0.5661 (tmt-80) REVERT: F 208 LYS cc_start: 0.4610 (mmmt) cc_final: 0.3955 (mttm) REVERT: F 283 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.5763 (tt0) REVERT: F 450 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7378 (ttpt) REVERT: F 459 TYR cc_start: 0.6828 (t80) cc_final: 0.6572 (t80) REVERT: G 179 MET cc_start: 0.7440 (ptt) cc_final: 0.7027 (ptt) REVERT: G 271 ILE cc_start: 0.7183 (pp) cc_final: 0.6881 (pp) REVERT: G 456 PHE cc_start: 0.8149 (t80) cc_final: 0.7545 (t80) REVERT: G 459 TYR cc_start: 0.6817 (t80) cc_final: 0.6596 (t80) REVERT: H 179 MET cc_start: 0.7433 (ptt) cc_final: 0.7039 (ptt) REVERT: H 283 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.5812 (tt0) REVERT: H 450 LYS cc_start: 0.7643 (ttmm) cc_final: 0.7266 (ttpt) outliers start: 94 outliers final: 55 residues processed: 514 average time/residue: 0.1643 time to fit residues: 138.1147 Evaluate side-chains 480 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 422 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.0010 chunk 358 optimal weight: 0.9980 chunk 218 optimal weight: 0.0870 chunk 224 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN D 102 ASN D 469 GLN E 102 ASN E 469 GLN F 102 ASN H 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.193784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.167862 restraints weight = 32876.830| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 1.79 r_work: 0.4216 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28800 Z= 0.120 Angle : 0.572 7.378 39176 Z= 0.285 Chirality : 0.043 0.160 4600 Planarity : 0.004 0.046 4800 Dihedral : 18.352 173.589 4928 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.69 % Allowed : 15.71 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3528 helix: 0.88 (0.15), residues: 1344 sheet: -0.51 (0.30), residues: 240 loop : -0.72 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 182 TYR 0.010 0.001 TYR A 459 PHE 0.009 0.001 PHE D 114 HIS 0.002 0.001 HIS D 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (28800) covalent geometry : angle 0.57234 / 0.28 (39176) hydrogen bonds : bond 0.03350 / 2.25 ( 1110) hydrogen bonds : angle 5.22013 / 3.67 ( 3114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 426 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4719 (mmmt) cc_final: 0.3927 (mttm) REVERT: A 283 GLN cc_start: 0.6256 (OUTLIER) cc_final: 0.5598 (tt0) REVERT: A 450 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7379 (ttpt) REVERT: B 179 MET cc_start: 0.7376 (ptt) cc_final: 0.7149 (ptt) REVERT: B 208 LYS cc_start: 0.4611 (mmmt) cc_final: 0.3835 (mttm) REVERT: B 283 GLN cc_start: 0.6330 (OUTLIER) cc_final: 0.5602 (tt0) REVERT: B 450 LYS cc_start: 0.7548 (ttpt) cc_final: 0.7157 (ttpt) REVERT: C 179 MET cc_start: 0.7382 (ptt) cc_final: 0.7144 (ptt) REVERT: C 208 LYS cc_start: 0.4732 (mmmt) cc_final: 0.3959 (mttm) REVERT: C 271 ILE cc_start: 0.7367 (pp) cc_final: 0.6998 (pp) REVERT: C 283 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.5768 (tt0) REVERT: C 450 LYS cc_start: 0.7788 (ttmm) cc_final: 0.7394 (ttpt) REVERT: D 179 MET cc_start: 0.7411 (ptt) cc_final: 0.7113 (ptt) REVERT: D 208 LYS cc_start: 0.4734 (mmmt) cc_final: 0.3987 (mttm) REVERT: D 271 ILE cc_start: 0.7321 (pp) cc_final: 0.6962 (pp) REVERT: D 283 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.5636 (tt0) REVERT: E 179 MET cc_start: 0.7389 (ptt) cc_final: 0.7145 (ptt) REVERT: E 182 ARG cc_start: 0.5813 (ttt-90) cc_final: 0.5320 (tmt-80) REVERT: E 208 LYS cc_start: 0.4672 (mmmt) cc_final: 0.3925 (mttm) REVERT: E 271 ILE cc_start: 0.7399 (pp) cc_final: 0.7090 (pp) REVERT: E 283 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.5636 (tt0) REVERT: E 450 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7371 (ttpt) REVERT: F 179 MET cc_start: 0.7400 (ptt) cc_final: 0.7176 (ptt) REVERT: F 208 LYS cc_start: 0.4717 (mmmt) cc_final: 0.3920 (mttm) REVERT: F 271 ILE cc_start: 0.7311 (pp) cc_final: 0.6951 (pp) REVERT: F 283 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5578 (tt0) REVERT: F 377 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7221 (mm) REVERT: F 450 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7372 (ttpt) REVERT: G 179 MET cc_start: 0.7368 (ptt) cc_final: 0.7077 (ptt) REVERT: G 271 ILE cc_start: 0.7277 (pp) cc_final: 0.7002 (pp) REVERT: G 283 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.5619 (tt0) REVERT: H 179 MET cc_start: 0.7430 (ptt) cc_final: 0.7166 (ptt) REVERT: H 182 ARG cc_start: 0.5798 (ttt-90) cc_final: 0.5346 (tmt-80) REVERT: H 271 ILE cc_start: 0.7314 (pp) cc_final: 0.6959 (pp) REVERT: H 283 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.5624 (tt0) REVERT: H 450 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7263 (ttpt) REVERT: H 459 TYR cc_start: 0.6605 (t80) cc_final: 0.6273 (t80) outliers start: 108 outliers final: 69 residues processed: 491 average time/residue: 0.1574 time to fit residues: 128.0833 Evaluate side-chains 466 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 388 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 27 optimal weight: 0.0570 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 324 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 203 optimal weight: 0.6980 chunk 241 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 368 GLN C 230 ASN D 368 GLN E 230 ASN E 368 GLN F 230 ASN G 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.195462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.168787 restraints weight = 32465.758| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 1.87 r_work: 0.4152 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4021 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28800 Z= 0.126 Angle : 0.570 6.686 39176 Z= 0.283 Chirality : 0.044 0.150 4600 Planarity : 0.004 0.044 4800 Dihedral : 17.742 179.291 4928 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.76 % Allowed : 16.56 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3528 helix: 0.75 (0.14), residues: 1376 sheet: -0.13 (0.26), residues: 280 loop : -0.93 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.008 0.001 TYR E 282 PHE 0.009 0.001 PHE G 24 HIS 0.002 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (28800) covalent geometry : angle 0.57016 / 0.28 (39176) hydrogen bonds : bond 0.03449 / 2.32 ( 1110) hydrogen bonds : angle 5.19769 / 3.66 ( 3114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 409 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4847 (mmmt) cc_final: 0.3986 (mttm) REVERT: A 271 ILE cc_start: 0.7452 (pp) cc_final: 0.7108 (pp) REVERT: A 283 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.5889 (tt0) REVERT: A 450 LYS cc_start: 0.7730 (ttmm) cc_final: 0.7400 (ttpt) REVERT: A 491 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6256 (tt0) REVERT: B 208 LYS cc_start: 0.4754 (mmmt) cc_final: 0.3909 (mttm) REVERT: B 283 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.5697 (tt0) REVERT: B 377 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7223 (mm) REVERT: B 491 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6116 (tt0) REVERT: C 136 ARG cc_start: 0.7405 (mmp-170) cc_final: 0.7182 (mmp-170) REVERT: C 208 LYS cc_start: 0.4837 (mmmt) cc_final: 0.4007 (mttm) REVERT: C 271 ILE cc_start: 0.7370 (pp) cc_final: 0.7117 (pp) REVERT: C 283 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.5856 (mt0) REVERT: C 450 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7449 (ttpt) REVERT: D 150 MET cc_start: 0.6450 (tpt) cc_final: 0.5840 (tpt) REVERT: D 179 MET cc_start: 0.7539 (ptt) cc_final: 0.7299 (ptt) REVERT: D 208 LYS cc_start: 0.4783 (mmmt) cc_final: 0.3986 (mttm) REVERT: D 271 ILE cc_start: 0.7342 (pp) cc_final: 0.7003 (pp) REVERT: D 283 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5792 (mt0) REVERT: E 208 LYS cc_start: 0.4750 (mmmt) cc_final: 0.3986 (mttm) REVERT: E 271 ILE cc_start: 0.7441 (pp) cc_final: 0.7154 (pp) REVERT: E 283 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5960 (mt0) REVERT: E 450 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7444 (ttpt) REVERT: F 208 LYS cc_start: 0.4843 (mmmt) cc_final: 0.4012 (mttm) REVERT: F 271 ILE cc_start: 0.7371 (pp) cc_final: 0.7079 (pp) REVERT: F 283 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5680 (tt0) REVERT: F 377 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7254 (mm) REVERT: F 450 LYS cc_start: 0.7805 (ttmm) cc_final: 0.7431 (ttpt) REVERT: G 271 ILE cc_start: 0.7339 (pp) cc_final: 0.7106 (pp) REVERT: G 283 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5643 (tt0) REVERT: H 182 ARG cc_start: 0.5892 (ttt-90) cc_final: 0.5610 (tmt-80) REVERT: H 271 ILE cc_start: 0.7348 (pp) cc_final: 0.7007 (pp) REVERT: H 283 GLN cc_start: 0.6399 (OUTLIER) cc_final: 0.5688 (tt0) REVERT: H 450 LYS cc_start: 0.7673 (ttmm) cc_final: 0.7356 (ttpt) outliers start: 110 outliers final: 81 residues processed: 495 average time/residue: 0.1629 time to fit residues: 133.2486 Evaluate side-chains 485 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 392 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 171 optimal weight: 2.9990 chunk 230 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 355 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.201191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.176203 restraints weight = 32427.954| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 1.71 r_work: 0.4276 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4144 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28800 Z= 0.127 Angle : 0.575 8.023 39176 Z= 0.285 Chirality : 0.044 0.182 4600 Planarity : 0.004 0.049 4800 Dihedral : 17.308 179.323 4928 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.96 % Allowed : 18.51 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.14), residues: 3528 helix: 0.81 (0.15), residues: 1376 sheet: -0.30 (0.27), residues: 264 loop : -0.97 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 182 TYR 0.007 0.001 TYR G 348 PHE 0.010 0.001 PHE H 24 HIS 0.002 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (28800) covalent geometry : angle 0.57499 / 0.29 (39176) hydrogen bonds : bond 0.03432 / 2.31 ( 1110) hydrogen bonds : angle 5.15402 / 3.64 ( 3114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 434 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4837 (mmmt) cc_final: 0.3955 (mttm) REVERT: A 283 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5845 (mt0) REVERT: A 450 LYS cc_start: 0.7665 (ttmm) cc_final: 0.7366 (ttpt) REVERT: A 459 TYR cc_start: 0.7015 (t80) cc_final: 0.6780 (t80) REVERT: A 491 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6074 (tt0) REVERT: B 208 LYS cc_start: 0.4874 (mmmt) cc_final: 0.4021 (mttm) REVERT: B 271 ILE cc_start: 0.7356 (pp) cc_final: 0.7130 (pp) REVERT: B 377 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7204 (mm) REVERT: B 459 TYR cc_start: 0.7045 (t80) cc_final: 0.6680 (t80) REVERT: B 491 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6171 (tt0) REVERT: C 208 LYS cc_start: 0.4825 (mmmt) cc_final: 0.3963 (mttm) REVERT: C 271 ILE cc_start: 0.7331 (pp) cc_final: 0.7087 (pp) REVERT: C 450 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7396 (ttpt) REVERT: C 459 TYR cc_start: 0.6805 (t80) cc_final: 0.6488 (t80) REVERT: D 208 LYS cc_start: 0.4828 (mmmt) cc_final: 0.3997 (mttm) REVERT: D 271 ILE cc_start: 0.7379 (pp) cc_final: 0.7118 (pp) REVERT: E 208 LYS cc_start: 0.4830 (mmmt) cc_final: 0.3992 (mttm) REVERT: E 271 ILE cc_start: 0.7386 (pp) cc_final: 0.7081 (pp) REVERT: E 450 LYS cc_start: 0.7668 (ttmm) cc_final: 0.7363 (ttpt) REVERT: E 459 TYR cc_start: 0.7070 (t80) cc_final: 0.6848 (t80) REVERT: F 208 LYS cc_start: 0.4890 (mmmt) cc_final: 0.4030 (mttm) REVERT: F 271 ILE cc_start: 0.7364 (pp) cc_final: 0.7080 (pp) REVERT: F 377 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7227 (mm) REVERT: F 450 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7380 (ttpt) REVERT: H 271 ILE cc_start: 0.7385 (pp) cc_final: 0.7065 (pp) REVERT: H 450 LYS cc_start: 0.7609 (ttmm) cc_final: 0.7320 (ttpt) outliers start: 116 outliers final: 86 residues processed: 521 average time/residue: 0.1565 time to fit residues: 136.3692 Evaluate side-chains 505 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 414 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 37 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 201 optimal weight: 0.3980 chunk 171 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 286 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN D 230 ASN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.197409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.174084 restraints weight = 32638.921| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.52 r_work: 0.4256 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4131 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28800 Z= 0.166 Angle : 0.633 7.575 39176 Z= 0.316 Chirality : 0.046 0.169 4600 Planarity : 0.005 0.055 4800 Dihedral : 17.050 175.011 4928 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.03 % Allowed : 19.19 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3528 helix: 0.60 (0.14), residues: 1344 sheet: -0.57 (0.29), residues: 240 loop : -0.92 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 224 TYR 0.009 0.002 TYR G 348 PHE 0.010 0.002 PHE D 90 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (28800) covalent geometry : angle 0.63256 / 0.32 (39176) hydrogen bonds : bond 0.03942 / 2.65 ( 1110) hydrogen bonds : angle 5.40532 / 3.81 ( 3114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 447 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.7747 (ptt) cc_final: 0.7477 (pmm) REVERT: A 208 LYS cc_start: 0.4969 (mmmt) cc_final: 0.4048 (mttm) REVERT: A 450 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7387 (ttpt) REVERT: A 459 TYR cc_start: 0.7104 (t80) cc_final: 0.6798 (t80) REVERT: B 208 LYS cc_start: 0.4978 (mmmt) cc_final: 0.4084 (mttm) REVERT: B 377 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7399 (mm) REVERT: B 459 TYR cc_start: 0.7016 (t80) cc_final: 0.6686 (t80) REVERT: C 208 LYS cc_start: 0.4980 (mmmt) cc_final: 0.4100 (mttm) REVERT: C 450 LYS cc_start: 0.7670 (ttmm) cc_final: 0.7398 (ttpt) REVERT: C 459 TYR cc_start: 0.6997 (t80) cc_final: 0.6708 (t80) REVERT: D 208 LYS cc_start: 0.4985 (mmmt) cc_final: 0.4082 (mttm) REVERT: D 271 ILE cc_start: 0.7397 (pp) cc_final: 0.7173 (pp) REVERT: E 208 LYS cc_start: 0.4972 (mmmt) cc_final: 0.4048 (mttm) REVERT: E 450 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7372 (ttpt) REVERT: E 459 TYR cc_start: 0.7114 (t80) cc_final: 0.6826 (t80) REVERT: F 208 LYS cc_start: 0.4946 (mmmt) cc_final: 0.4084 (mttm) REVERT: F 450 LYS cc_start: 0.7642 (ttmm) cc_final: 0.7419 (ttpt) REVERT: G 459 TYR cc_start: 0.7001 (t80) cc_final: 0.6681 (t80) REVERT: H 450 LYS cc_start: 0.7595 (ttmm) cc_final: 0.7360 (ttpt) outliers start: 118 outliers final: 84 residues processed: 535 average time/residue: 0.1610 time to fit residues: 142.4757 Evaluate side-chains 518 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 433 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 349 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 0.0270 chunk 130 optimal weight: 0.6980 chunk 318 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.187896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.161476 restraints weight = 33561.167| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 1.86 r_work: 0.4140 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28800 Z= 0.139 Angle : 0.611 7.683 39176 Z= 0.304 Chirality : 0.044 0.164 4600 Planarity : 0.004 0.059 4800 Dihedral : 16.638 178.304 4928 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.35 % Allowed : 20.70 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3528 helix: 0.55 (0.14), residues: 1384 sheet: -0.50 (0.27), residues: 264 loop : -1.10 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 182 TYR 0.008 0.001 TYR F 459 PHE 0.009 0.002 PHE C 90 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (28800) covalent geometry : angle 0.61058 / 0.30 (39176) hydrogen bonds : bond 0.03585 / 2.41 ( 1110) hydrogen bonds : angle 5.27114 / 3.73 ( 3114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 438 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4848 (mmmt) cc_final: 0.3890 (mttm) REVERT: A 450 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7435 (ttpt) REVERT: A 459 TYR cc_start: 0.7134 (t80) cc_final: 0.6820 (t80) REVERT: A 491 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6264 (tt0) REVERT: B 208 LYS cc_start: 0.4925 (mmmt) cc_final: 0.3945 (mttm) REVERT: B 283 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.6030 (mt0) REVERT: B 377 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7277 (mm) REVERT: B 459 TYR cc_start: 0.6999 (t80) cc_final: 0.6661 (t80) REVERT: B 491 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6217 (tt0) REVERT: C 208 LYS cc_start: 0.5038 (mmmt) cc_final: 0.3933 (mttm) REVERT: C 271 ILE cc_start: 0.7370 (pp) cc_final: 0.7089 (pp) REVERT: C 283 GLN cc_start: 0.6523 (OUTLIER) cc_final: 0.6108 (mt0) REVERT: C 450 LYS cc_start: 0.7707 (ttmm) cc_final: 0.7381 (ttpt) REVERT: C 459 TYR cc_start: 0.7083 (t80) cc_final: 0.6773 (t80) REVERT: D 208 LYS cc_start: 0.4831 (mmmt) cc_final: 0.3891 (mttm) REVERT: D 271 ILE cc_start: 0.7424 (pp) cc_final: 0.7218 (pp) REVERT: D 283 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6017 (mt0) REVERT: D 491 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6168 (tt0) REVERT: E 208 LYS cc_start: 0.4833 (mmmt) cc_final: 0.3886 (mttm) REVERT: E 286 MET cc_start: 0.7900 (tpt) cc_final: 0.7663 (tpt) REVERT: E 450 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7403 (ttpt) REVERT: E 459 TYR cc_start: 0.7197 (t80) cc_final: 0.6881 (t80) REVERT: F 208 LYS cc_start: 0.4863 (mmmt) cc_final: 0.3911 (mttm) REVERT: F 271 ILE cc_start: 0.7467 (pp) cc_final: 0.7181 (pp) REVERT: F 283 GLN cc_start: 0.6433 (OUTLIER) cc_final: 0.6073 (mt0) REVERT: F 377 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7287 (mm) REVERT: F 450 LYS cc_start: 0.7701 (ttmm) cc_final: 0.7397 (ttpt) REVERT: G 459 TYR cc_start: 0.7047 (t80) cc_final: 0.6720 (t80) REVERT: H 271 ILE cc_start: 0.7482 (pp) cc_final: 0.7200 (pp) REVERT: H 450 LYS cc_start: 0.7615 (ttmm) cc_final: 0.7298 (ttpt) REVERT: H 491 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6190 (tt0) outliers start: 98 outliers final: 84 residues processed: 516 average time/residue: 0.1574 time to fit residues: 137.0941 Evaluate side-chains 518 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 424 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 156 optimal weight: 3.9990 chunk 315 optimal weight: 0.0170 chunk 336 optimal weight: 0.4980 chunk 96 optimal weight: 0.1980 chunk 230 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.190052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.162768 restraints weight = 33316.715| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 1.95 r_work: 0.4166 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4036 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28800 Z= 0.112 Angle : 0.581 7.600 39176 Z= 0.288 Chirality : 0.043 0.146 4600 Planarity : 0.004 0.060 4800 Dihedral : 15.764 179.696 4928 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.52 % Allowed : 21.00 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3528 helix: 0.79 (0.14), residues: 1384 sheet: -0.21 (0.27), residues: 264 loop : -0.95 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 182 TYR 0.008 0.001 TYR F 459 PHE 0.008 0.001 PHE H 24 HIS 0.002 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (28800) covalent geometry : angle 0.58050 / 0.29 (39176) hydrogen bonds : bond 0.03240 / 2.18 ( 1110) hydrogen bonds : angle 5.09968 / 3.60 ( 3114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 447 time to evaluate : 1.143 Fit side-chains REVERT: A 208 LYS cc_start: 0.4798 (mmmt) cc_final: 0.3847 (mttm) REVERT: A 450 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7354 (ttpt) REVERT: A 459 TYR cc_start: 0.7147 (t80) cc_final: 0.6825 (t80) REVERT: A 491 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: B 208 LYS cc_start: 0.4840 (mmmt) cc_final: 0.3874 (mttm) REVERT: B 271 ILE cc_start: 0.7505 (pp) cc_final: 0.7274 (pp) REVERT: B 283 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.5774 (mt0) REVERT: B 377 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7229 (mm) REVERT: B 459 TYR cc_start: 0.7015 (t80) cc_final: 0.6655 (t80) REVERT: C 208 LYS cc_start: 0.4917 (mmmt) cc_final: 0.3870 (mttm) REVERT: C 450 LYS cc_start: 0.7713 (ttmm) cc_final: 0.7340 (ttpt) REVERT: C 459 TYR cc_start: 0.6998 (t80) cc_final: 0.6710 (t80) REVERT: D 150 MET cc_start: 0.6501 (tpt) cc_final: 0.5783 (tpt) REVERT: D 208 LYS cc_start: 0.4752 (mmmt) cc_final: 0.3834 (mttm) REVERT: D 271 ILE cc_start: 0.7623 (pp) cc_final: 0.7414 (pp) REVERT: D 283 GLN cc_start: 0.6366 (OUTLIER) cc_final: 0.5645 (tt0) REVERT: E 208 LYS cc_start: 0.4878 (mmmt) cc_final: 0.3809 (mttm) REVERT: E 450 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7356 (ttpt) REVERT: F 208 LYS cc_start: 0.4783 (mmmt) cc_final: 0.3855 (mttm) REVERT: F 283 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5742 (mt0) REVERT: F 377 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7210 (mm) REVERT: F 450 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7307 (ttpt) REVERT: G 166 LEU cc_start: 0.6691 (mp) cc_final: 0.5983 (mt) REVERT: G 283 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.5612 (tt0) REVERT: G 459 TYR cc_start: 0.7040 (t80) cc_final: 0.6698 (t80) REVERT: H 271 ILE cc_start: 0.7495 (pp) cc_final: 0.7275 (pp) REVERT: H 283 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5652 (tt0) REVERT: H 450 LYS cc_start: 0.7729 (ttmm) cc_final: 0.7319 (ttpt) outliers start: 103 outliers final: 85 residues processed: 526 average time/residue: 0.1521 time to fit residues: 134.8557 Evaluate side-chains 518 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 425 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 22 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 249 optimal weight: 0.3980 chunk 354 optimal weight: 0.9980 chunk 318 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 307 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.188921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.162637 restraints weight = 33206.760| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 1.85 r_work: 0.4153 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28800 Z= 0.135 Angle : 0.609 7.724 39176 Z= 0.302 Chirality : 0.044 0.178 4600 Planarity : 0.005 0.061 4800 Dihedral : 15.449 179.755 4928 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.24 % Allowed : 21.45 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3528 helix: 0.72 (0.14), residues: 1384 sheet: -0.32 (0.27), residues: 264 loop : -1.03 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 182 TYR 0.011 0.001 TYR G 289 PHE 0.008 0.001 PHE G 90 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (28800) covalent geometry : angle 0.60865 / 0.30 (39176) hydrogen bonds : bond 0.03532 / 2.38 ( 1110) hydrogen bonds : angle 5.20433 / 3.68 ( 3114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 427 time to evaluate : 0.995 Fit side-chains REVERT: A 208 LYS cc_start: 0.5059 (mmmt) cc_final: 0.3887 (mttm) REVERT: A 450 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7396 (ttpt) REVERT: A 491 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6533 (tt0) REVERT: B 208 LYS cc_start: 0.4892 (mmmt) cc_final: 0.3937 (mttm) REVERT: B 377 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7290 (mm) REVERT: B 459 TYR cc_start: 0.7033 (t80) cc_final: 0.6678 (t80) REVERT: B 491 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6439 (tt0) REVERT: C 208 LYS cc_start: 0.4997 (mmmt) cc_final: 0.3937 (mttm) REVERT: C 450 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7330 (ttpt) REVERT: C 459 TYR cc_start: 0.7003 (t80) cc_final: 0.6721 (t80) REVERT: D 208 LYS cc_start: 0.4992 (mmmt) cc_final: 0.3882 (mttm) REVERT: D 491 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6214 (tt0) REVERT: E 208 LYS cc_start: 0.4941 (mmmt) cc_final: 0.3846 (mttm) REVERT: E 450 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7352 (ttpt) REVERT: F 208 LYS cc_start: 0.4821 (mmmt) cc_final: 0.3910 (mttm) REVERT: F 283 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.5837 (mt0) REVERT: F 377 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7345 (mm) REVERT: F 450 LYS cc_start: 0.7681 (ttmm) cc_final: 0.7344 (ttpt) REVERT: F 491 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: G 166 LEU cc_start: 0.6675 (mp) cc_final: 0.5941 (mt) REVERT: G 283 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6030 (mt0) REVERT: G 459 TYR cc_start: 0.7046 (t80) cc_final: 0.6721 (t80) REVERT: H 283 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5893 (mt0) REVERT: H 450 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7330 (ttpt) outliers start: 95 outliers final: 84 residues processed: 497 average time/residue: 0.1525 time to fit residues: 127.9009 Evaluate side-chains 513 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 420 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 282 optimal weight: 7.9990 chunk 309 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 203 optimal weight: 0.0570 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.190780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.162946 restraints weight = 32890.972| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 1.95 r_work: 0.4138 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28800 Z= 0.143 Angle : 0.619 7.665 39176 Z= 0.307 Chirality : 0.044 0.193 4600 Planarity : 0.005 0.062 4800 Dihedral : 15.302 179.705 4928 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.38 % Allowed : 21.17 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3528 helix: 0.68 (0.14), residues: 1384 sheet: -0.40 (0.27), residues: 264 loop : -1.07 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 182 TYR 0.008 0.001 TYR A 459 PHE 0.009 0.002 PHE C 90 HIS 0.002 0.001 HIS D 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (28800) covalent geometry : angle 0.61935 / 0.31 (39176) hydrogen bonds : bond 0.03593 / 2.43 ( 1110) hydrogen bonds : angle 5.23634 / 3.70 ( 3114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7940.88 seconds wall clock time: 136 minutes 32.26 seconds (8192.26 seconds total)