Starting phenix.real_space_refine on Mon Aug 25 14:23:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7m_41986/08_2025/8u7m_41986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7m_41986/08_2025/8u7m_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u7m_41986/08_2025/8u7m_41986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7m_41986/08_2025/8u7m_41986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u7m_41986/08_2025/8u7m_41986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7m_41986/08_2025/8u7m_41986.map" } 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-2.0-5787/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, 'NAD': 1} Classifications: {'RNA': 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, 'NAD': 1} Classifications: {'RNA': 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, 'NAD': 1} Classifications: {'RNA': 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, 'NAD': 1} Classifications: {'RNA': 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, 'NAD': 1} Classifications: {'RNA': 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, 'NAD': 1} Classifications: {'RNA': 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, 'NAD': 1} Classifications: {'RNA': 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, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 6.32, per 1000 atoms: 0.22 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.16 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: 5.66 Time building geometry restraints manager: 3.31 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=" C5 IMP F 604 " pdb=" C6 IMP F 604 " ideal model delta sigma weight residual 1.390 1.532 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C5 IMP G 604 " pdb=" C6 IMP G 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C5 IMP D 604 " pdb=" C6 IMP D 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C5 IMP B 604 " pdb=" C6 IMP B 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C5 IMP H 604 " pdb=" C6 IMP H 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.98e+01 ... (remaining 28795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 38654 3.87 - 7.74: 339 7.74 - 11.62: 147 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 - 35.57: 16912 35.57 - 71.14: 588 71.14 - 106.71: 97 106.71 - 142.28: 39 142.28 - 177.84: 12 Dihedral angle restraints: 17648 sinusoidal: 7488 harmonic: 10160 Sorted by residual: dihedral pdb=" C5' IMP A 604 " pdb=" O5' IMP A 604 " pdb=" P IMP A 604 " pdb=" O2P IMP A 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.09 177.84 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP D 604 " pdb=" O5' IMP D 604 " pdb=" P IMP D 604 " pdb=" O2P IMP D 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.31 177.62 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP B 604 " pdb=" O5' IMP B 604 " pdb=" P IMP B 604 " pdb=" O2P IMP B 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.43 177.50 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 17645 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: 0.02 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: 5.490 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.240 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- 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 0.142 28800 Z= 0.331 Angle : 1.135 19.362 39176 Z= 0.567 Chirality : 0.088 1.699 4600 Planarity : 0.006 0.104 4800 Dihedral : 20.220 177.844 11136 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 aren 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 covalent geometry : bond 0.00658 (28800) covalent geometry : angle 1.13481 (39176) hydrogen bonds : bond 0.14852 ( 1110) hydrogen bonds : angle 6.90590 ( 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 : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 507 average time/residue: 0.1718 time to fit residues: 142.9233 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 : 1.095 ------------------------------------------------------------------------------- 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: 0.6980 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 = 0.4584 r_free = 0.4584 target = 0.198563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.171584 restraints weight = 32652.281| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 1.85 r_work: 0.4249 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.1356 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 : 0.639 7.213 39176 Z= 0.317 Chirality : 0.045 0.184 4600 Planarity : 0.005 0.063 4800 Dihedral : 20.989 151.781 4800 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.88 % Allowed : 15.81 % Favored : 82.31 % 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 aren not related in a simple way. whole: -0.61 (0.14), residues: 3528 helix: 0.39 (0.14), residues: 1400 sheet: -0.56 (0.32), residues: 240 loop : -0.97 (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 0.017 0.002 PHE A 456 HIS 0.005 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00267 (28800) covalent geometry : angle 0.63939 (39176) hydrogen bonds : bond 0.03536 ( 1110) hydrogen bonds : angle 5.48678 ( 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 543 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 488 time to evaluate : 1.059 Fit side-chains REVERT: A 105 ARG cc_start: 0.6094 (OUTLIER) cc_final: 0.5852 (mpt-90) REVERT: A 182 ARG cc_start: 0.5751 (ttt-90) cc_final: 0.5392 (ttt-90) REVERT: A 353 TYR cc_start: 0.7158 (t80) cc_final: 0.6812 (t80) REVERT: A 450 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7180 (ttpt) REVERT: B 105 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.5737 (mpt-90) REVERT: B 179 MET cc_start: 0.7511 (ptt) cc_final: 0.7073 (ptt) REVERT: B 450 LYS cc_start: 0.7747 (ttmm) cc_final: 0.7193 (ttpt) REVERT: C 105 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.5684 (mpt-90) REVERT: C 179 MET cc_start: 0.7511 (ptt) cc_final: 0.7054 (ptt) REVERT: C 450 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7163 (ttpt) REVERT: D 105 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5870 (mpt-90) REVERT: D 179 MET cc_start: 0.7548 (ptt) cc_final: 0.7057 (ptt) REVERT: D 182 ARG cc_start: 0.5789 (ttt-90) cc_final: 0.5348 (ttt-90) REVERT: D 353 TYR cc_start: 0.7171 (t80) cc_final: 0.6821 (t80) REVERT: D 450 LYS cc_start: 0.7645 (ttmm) cc_final: 0.7087 (ttpt) REVERT: E 105 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5865 (mpt-90) REVERT: E 179 MET cc_start: 0.7505 (ptt) cc_final: 0.7080 (ptt) REVERT: E 182 ARG cc_start: 0.5665 (ttt-90) cc_final: 0.5227 (ttt-90) REVERT: E 353 TYR cc_start: 0.7182 (t80) cc_final: 0.6835 (t80) REVERT: E 450 LYS cc_start: 0.7822 (ttmm) cc_final: 0.7150 (ttpt) REVERT: F 105 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.5751 (mpt-90) REVERT: F 179 MET cc_start: 0.7455 (ptt) cc_final: 0.7023 (ptt) REVERT: F 353 TYR cc_start: 0.7186 (t80) cc_final: 0.6846 (t80) REVERT: F 450 LYS cc_start: 0.7677 (ttmm) cc_final: 0.7127 (ttpt) REVERT: G 105 ARG cc_start: 0.5896 (OUTLIER) cc_final: 0.5677 (mpt-90) REVERT: G 179 MET cc_start: 0.7490 (ptt) cc_final: 0.7042 (ptt) REVERT: G 450 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7171 (ttpt) REVERT: H 105 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.5877 (mpt-90) REVERT: H 179 MET cc_start: 0.7461 (ptt) cc_final: 0.7035 (ptt) REVERT: H 353 TYR cc_start: 0.7187 (t80) cc_final: 0.6836 (t80) outliers start: 55 outliers final: 20 residues processed: 521 average time/residue: 0.1711 time to fit residues: 145.7954 Evaluate side-chains 463 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 435 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 310 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 166 optimal weight: 0.0060 chunk 263 optimal weight: 0.9990 chunk 358 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 303 optimal weight: 0.4980 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 = 0.4520 r_free = 0.4520 target = 0.191998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.165060 restraints weight = 32922.714| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 1.86 r_work: 0.4124 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3993 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28800 Z= 0.159 Angle : 0.644 6.553 39176 Z= 0.323 Chirality : 0.046 0.184 4600 Planarity : 0.005 0.051 4800 Dihedral : 19.434 149.488 4800 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.20 % Allowed : 14.96 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.14), residues: 3528 helix: 0.44 (0.14), residues: 1344 sheet: -0.63 (0.28), residues: 264 loop : -0.96 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.019 0.002 TYR A 459 PHE 0.013 0.002 PHE F 114 HIS 0.003 0.001 HIS C 466 Details of bonding type rmsd covalent geometry : bond 0.00383 (28800) covalent geometry : angle 0.64359 (39176) hydrogen bonds : bond 0.04105 ( 1110) hydrogen bonds : angle 5.52968 ( 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 585 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 462 time to evaluate : 1.066 Fit side-chains REVERT: A 105 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.4058 (tpt-90) REVERT: A 182 ARG cc_start: 0.5907 (ttt-90) cc_final: 0.5610 (ttt-90) REVERT: A 208 LYS cc_start: 0.4821 (mmmt) cc_final: 0.3981 (mttm) REVERT: A 450 LYS cc_start: 0.7781 (ttmm) cc_final: 0.7368 (ttpt) REVERT: A 459 TYR cc_start: 0.6913 (t80) cc_final: 0.6618 (t80) REVERT: A 461 ILE cc_start: 0.5539 (mp) cc_final: 0.5224 (mm) REVERT: B 105 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.4099 (tpt-90) REVERT: B 179 MET cc_start: 0.7488 (ptt) cc_final: 0.6999 (ptt) REVERT: B 208 LYS cc_start: 0.4817 (mmmt) cc_final: 0.3943 (mttm) REVERT: B 450 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7422 (ttpt) REVERT: B 459 TYR cc_start: 0.6901 (t80) cc_final: 0.6582 (t80) REVERT: C 179 MET cc_start: 0.7493 (ptt) cc_final: 0.7004 (ptt) REVERT: C 182 ARG cc_start: 0.5868 (ttt-90) cc_final: 0.5567 (ttt-90) REVERT: C 208 LYS cc_start: 0.4858 (mmmt) cc_final: 0.4020 (mttm) REVERT: C 450 LYS cc_start: 0.7856 (ttmm) cc_final: 0.7397 (ttpt) REVERT: C 459 TYR cc_start: 0.6828 (t80) cc_final: 0.6556 (t80) REVERT: D 105 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.4054 (tpt-90) REVERT: D 179 MET cc_start: 0.7549 (ptt) cc_final: 0.7029 (ptt) REVERT: D 208 LYS cc_start: 0.4842 (mmmt) cc_final: 0.4044 (mttm) REVERT: D 450 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7398 (ttpt) REVERT: D 459 TYR cc_start: 0.6787 (t80) cc_final: 0.6509 (t80) REVERT: E 105 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.4045 (tpt-90) REVERT: E 179 MET cc_start: 0.7482 (ptt) cc_final: 0.7040 (ptt) REVERT: E 208 LYS cc_start: 0.4798 (mmmt) cc_final: 0.3986 (mttm) REVERT: E 450 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7321 (ttpt) REVERT: E 459 TYR cc_start: 0.6866 (t80) cc_final: 0.6593 (t80) REVERT: E 461 ILE cc_start: 0.5556 (mp) cc_final: 0.5272 (mm) REVERT: F 105 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.4080 (tpt-90) REVERT: F 179 MET cc_start: 0.7495 (ptt) cc_final: 0.7051 (ptt) REVERT: F 182 ARG cc_start: 0.5945 (ttt-90) cc_final: 0.5650 (ttt-90) REVERT: F 208 LYS cc_start: 0.4833 (mmmt) cc_final: 0.4008 (mttm) REVERT: F 450 LYS cc_start: 0.7872 (ttmm) cc_final: 0.7379 (ttpt) REVERT: F 459 TYR cc_start: 0.6925 (t80) cc_final: 0.6627 (t80) REVERT: G 179 MET cc_start: 0.7457 (ptt) cc_final: 0.7007 (ptt) REVERT: G 450 LYS cc_start: 0.7872 (ttmm) cc_final: 0.7415 (ttpt) REVERT: G 459 TYR cc_start: 0.6830 (t80) cc_final: 0.6562 (t80) REVERT: H 105 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.4060 (tpt-90) REVERT: H 179 MET cc_start: 0.7445 (ptt) cc_final: 0.7012 (ptt) REVERT: H 450 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7280 (ttpt) outliers start: 123 outliers final: 85 residues processed: 545 average time/residue: 0.1738 time to fit residues: 155.2346 Evaluate side-chains 523 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 432 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 318 VAL 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 B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 105 ARG 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 318 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 367 ILE 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 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 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 367 ILE 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 105 ARG 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 E residue 45 ILE Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 283 GLN 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 F residue 45 ILE Chi-restraints excluded: chain F residue 105 ARG 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 367 ILE 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 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 367 ILE 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 105 ARG 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 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 367 ILE 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: 3.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 218 optimal weight: 0.4980 chunk 224 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN C 368 GLN D 368 GLN E 368 GLN G 368 GLN H 102 ASN H 368 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.190967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.164500 restraints weight = 33104.499| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 1.87 r_work: 0.4119 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28800 Z= 0.143 Angle : 0.599 6.981 39176 Z= 0.299 Chirality : 0.044 0.158 4600 Planarity : 0.005 0.047 4800 Dihedral : 18.618 175.708 4800 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.27 % Allowed : 15.47 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.14), residues: 3528 helix: 0.49 (0.14), residues: 1384 sheet: -0.89 (0.31), residues: 224 loop : -1.04 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 182 TYR 0.010 0.001 TYR E 459 PHE 0.010 0.002 PHE D 114 HIS 0.003 0.001 HIS D 288 Details of bonding type rmsd covalent geometry : bond 0.00340 (28800) covalent geometry : angle 0.59909 (39176) hydrogen bonds : bond 0.03700 ( 1110) hydrogen bonds : angle 5.38200 ( 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 577 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 452 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.5014 (mmmt) cc_final: 0.3936 (mttm) REVERT: A 450 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7341 (ttpt) REVERT: B 179 MET cc_start: 0.7594 (ptt) cc_final: 0.7341 (ptt) REVERT: B 208 LYS cc_start: 0.4903 (mmmt) cc_final: 0.4005 (mttm) REVERT: B 283 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.5811 (tt0) REVERT: B 450 LYS cc_start: 0.7791 (ttmm) cc_final: 0.7406 (ttpt) REVERT: B 459 TYR cc_start: 0.7147 (t80) cc_final: 0.6886 (t80) REVERT: B 491 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6098 (tt0) REVERT: C 179 MET cc_start: 0.7552 (ptt) cc_final: 0.7268 (ptt) REVERT: C 208 LYS cc_start: 0.4875 (mmmt) cc_final: 0.3945 (mttm) REVERT: C 450 LYS cc_start: 0.7868 (ttmm) cc_final: 0.7447 (ttpt) REVERT: C 459 TYR cc_start: 0.7188 (t80) cc_final: 0.6960 (t80) REVERT: D 179 MET cc_start: 0.7612 (ptt) cc_final: 0.7283 (ptt) REVERT: D 182 ARG cc_start: 0.6115 (ttt-90) cc_final: 0.5486 (tmt-80) REVERT: D 208 LYS cc_start: 0.4862 (mmmt) cc_final: 0.3973 (mttm) REVERT: D 459 TYR cc_start: 0.7127 (t80) cc_final: 0.6866 (t80) REVERT: E 179 MET cc_start: 0.7553 (ptt) cc_final: 0.7264 (ptt) REVERT: E 208 LYS cc_start: 0.4828 (mmmt) cc_final: 0.3998 (mttm) REVERT: E 283 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.5805 (tt0) REVERT: E 450 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7427 (ttpt) REVERT: F 179 MET cc_start: 0.7570 (ptt) cc_final: 0.7333 (ptt) REVERT: F 208 LYS cc_start: 0.4917 (mmmt) cc_final: 0.4016 (mttm) REVERT: F 283 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.5685 (tt0) REVERT: F 377 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7272 (mm) REVERT: F 450 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7428 (ttpt) REVERT: F 459 TYR cc_start: 0.7148 (t80) cc_final: 0.6872 (t80) REVERT: G 179 MET cc_start: 0.7595 (ptt) cc_final: 0.7288 (ptt) REVERT: G 271 ILE cc_start: 0.7472 (pp) cc_final: 0.7179 (pp) REVERT: G 450 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7420 (ttpt) REVERT: G 459 TYR cc_start: 0.7151 (t80) cc_final: 0.6884 (t80) REVERT: H 179 MET cc_start: 0.7589 (ptt) cc_final: 0.7319 (ptt) REVERT: H 182 ARG cc_start: 0.5907 (ttt-90) cc_final: 0.5649 (tmt-80) REVERT: H 283 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.5974 (mt0) REVERT: H 450 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7279 (ttpt) REVERT: H 459 TYR cc_start: 0.6674 (t80) cc_final: 0.6358 (t80) outliers start: 125 outliers final: 76 residues processed: 539 average time/residue: 0.1718 time to fit residues: 148.9887 Evaluate side-chains 494 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 412 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 282 TYR 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 491 GLU 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 491 GLU 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 C residue 491 GLU 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 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 491 GLU 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 282 TYR Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL 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 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 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 491 GLU 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 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 324 optimal weight: 2.9990 chunk 357 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 191 optimal weight: 0.0570 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN H 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.194129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.171826 restraints weight = 32833.896| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.43 r_work: 0.4237 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28800 Z= 0.185 Angle : 0.651 7.932 39176 Z= 0.327 Chirality : 0.047 0.183 4600 Planarity : 0.005 0.045 4800 Dihedral : 18.180 179.430 4800 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.17 % Allowed : 16.91 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.14), residues: 3528 helix: 0.29 (0.14), residues: 1336 sheet: -0.71 (0.27), residues: 264 loop : -1.10 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 182 TYR 0.009 0.002 TYR F 348 PHE 0.011 0.002 PHE A 90 HIS 0.003 0.001 HIS G 288 Details of bonding type rmsd covalent geometry : bond 0.00442 (28800) covalent geometry : angle 0.65071 (39176) hydrogen bonds : bond 0.04305 ( 1110) hydrogen bonds : angle 5.64377 ( 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 573 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 451 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 450 LYS cc_start: 0.7689 (ttmm) cc_final: 0.7367 (ttpt) REVERT: B 136 ARG cc_start: 0.7435 (mmp-170) cc_final: 0.7206 (mmp-170) REVERT: B 208 LYS cc_start: 0.5027 (mmmt) cc_final: 0.4122 (mttm) REVERT: B 377 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7451 (mm) REVERT: B 450 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7391 (ttpt) REVERT: B 459 TYR cc_start: 0.7069 (t80) cc_final: 0.6799 (t80) REVERT: B 491 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6119 (tt0) REVERT: C 179 MET cc_start: 0.7620 (ptt) cc_final: 0.7392 (ptt) REVERT: C 208 LYS cc_start: 0.5141 (mmmt) cc_final: 0.4098 (mttm) REVERT: C 450 LYS cc_start: 0.7642 (ttmm) cc_final: 0.7393 (ttpt) REVERT: C 459 TYR cc_start: 0.7063 (t80) cc_final: 0.6802 (t80) REVERT: D 182 ARG cc_start: 0.6248 (ttt-90) cc_final: 0.5800 (tmt-80) REVERT: D 208 LYS cc_start: 0.5147 (mmmt) cc_final: 0.4094 (mttm) REVERT: D 450 LYS cc_start: 0.7749 (ttmm) cc_final: 0.7368 (ttpt) REVERT: D 459 TYR cc_start: 0.7132 (t80) cc_final: 0.6855 (t80) REVERT: E 208 LYS cc_start: 0.4976 (mmmt) cc_final: 0.4086 (mttm) REVERT: E 450 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7356 (ttpt) REVERT: F 208 LYS cc_start: 0.5028 (mmmt) cc_final: 0.4125 (mttm) REVERT: F 450 LYS cc_start: 0.7708 (ttmm) cc_final: 0.7399 (ttpt) REVERT: F 459 TYR cc_start: 0.7107 (t80) cc_final: 0.6858 (t80) REVERT: G 450 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7397 (ttpt) REVERT: G 459 TYR cc_start: 0.7115 (t80) cc_final: 0.6888 (t80) REVERT: H 182 ARG cc_start: 0.6071 (ttt-90) cc_final: 0.5868 (tmt-80) REVERT: H 450 LYS cc_start: 0.7632 (ttmm) cc_final: 0.7408 (ttpt) REVERT: H 459 TYR cc_start: 0.7041 (t80) cc_final: 0.6799 (t80) outliers start: 122 outliers final: 83 residues processed: 543 average time/residue: 0.1859 time to fit residues: 165.7466 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 : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 282 TYR Chi-restraints excluded: chain A residue 318 VAL 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 94 ASN 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 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 67 SER 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 94 ASN Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 318 VAL 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 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 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 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 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 209 LEU 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 333 THR 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: 0.5980 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 355 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 0.0670 chunk 65 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.4630 r_free = 0.4630 target = 0.197787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.173656 restraints weight = 32727.137| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 1.65 r_work: 0.4256 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3507 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= 0.123 Angle : 0.595 7.629 39176 Z= 0.297 Chirality : 0.044 0.163 4600 Planarity : 0.004 0.054 4800 Dihedral : 17.806 177.276 4800 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.28 % Allowed : 20.22 % Favored : 76.50 % 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 aren not related in a simple way. whole: -0.43 (0.14), residues: 3528 helix: 0.71 (0.15), residues: 1336 sheet: -0.65 (0.29), residues: 240 loop : -0.94 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 182 TYR 0.007 0.001 TYR E 282 PHE 0.009 0.001 PHE C 90 HIS 0.002 0.000 HIS G 288 Details of bonding type rmsd covalent geometry : bond 0.00288 (28800) covalent geometry : angle 0.59504 (39176) hydrogen bonds : bond 0.03551 ( 1110) hydrogen bonds : angle 5.26823 ( 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 549 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 453 time to evaluate : 1.156 Fit side-chains REVERT: A 208 LYS cc_start: 0.5052 (mmmt) cc_final: 0.4040 (mttm) REVERT: A 450 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7377 (ttpt) REVERT: B 208 LYS cc_start: 0.4978 (mmmt) cc_final: 0.4100 (mttm) REVERT: B 283 GLN cc_start: 0.6194 (OUTLIER) cc_final: 0.5731 (mt0) REVERT: B 377 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7216 (mm) REVERT: B 450 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7372 (ttpt) REVERT: B 459 TYR cc_start: 0.7107 (t80) cc_final: 0.6849 (t80) REVERT: B 491 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6064 (tt0) REVERT: C 208 LYS cc_start: 0.5049 (mmmt) cc_final: 0.4079 (mttm) REVERT: C 283 GLN cc_start: 0.6382 (OUTLIER) cc_final: 0.5981 (mt0) REVERT: C 450 LYS cc_start: 0.7663 (ttmm) cc_final: 0.7384 (ttpt) REVERT: C 459 TYR cc_start: 0.7101 (t80) cc_final: 0.6854 (t80) REVERT: D 208 LYS cc_start: 0.5044 (mmmt) cc_final: 0.4050 (mttm) REVERT: D 271 ILE cc_start: 0.7384 (pp) cc_final: 0.7168 (pp) REVERT: D 283 GLN cc_start: 0.6295 (OUTLIER) cc_final: 0.5796 (mt0) REVERT: D 450 LYS cc_start: 0.7744 (ttmm) cc_final: 0.7431 (ttpt) REVERT: D 459 TYR cc_start: 0.7124 (t80) cc_final: 0.6822 (t80) REVERT: E 208 LYS cc_start: 0.4890 (mmmt) cc_final: 0.4061 (mttm) REVERT: E 217 GLU cc_start: 0.4604 (mp0) cc_final: 0.3954 (mp0) REVERT: E 271 ILE cc_start: 0.7385 (pp) cc_final: 0.7170 (pp) REVERT: E 450 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7354 (ttpt) REVERT: F 208 LYS cc_start: 0.4940 (mmmt) cc_final: 0.4077 (mttm) REVERT: F 271 ILE cc_start: 0.7391 (pp) cc_final: 0.7170 (pp) REVERT: F 283 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5794 (mt0) REVERT: F 377 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7218 (mm) REVERT: F 450 LYS cc_start: 0.7638 (ttmm) cc_final: 0.7366 (ttpt) REVERT: F 459 TYR cc_start: 0.7108 (t80) cc_final: 0.6848 (t80) REVERT: G 450 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7383 (ttpt) REVERT: G 459 TYR cc_start: 0.7191 (t80) cc_final: 0.6980 (t80) REVERT: H 182 ARG cc_start: 0.6299 (ttt-90) cc_final: 0.6095 (tmt-80) REVERT: H 271 ILE cc_start: 0.7388 (pp) cc_final: 0.7164 (pp) REVERT: H 283 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.5592 (tt0) REVERT: H 450 LYS cc_start: 0.7617 (ttmm) cc_final: 0.7373 (ttpt) REVERT: H 459 TYR cc_start: 0.7083 (t80) cc_final: 0.6822 (t80) outliers start: 96 outliers final: 82 residues processed: 526 average time/residue: 0.1798 time to fit residues: 156.8683 Evaluate side-chains 536 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 446 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 327 CYS 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 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN 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 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 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 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 460 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain F residue 37 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 395 GLU 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 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 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 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 208 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4418 r_free = 0.4418 target = 0.183381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.155629 restraints weight = 33542.548| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.94 r_work: 0.4004 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3872 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 28800 Z= 0.254 Angle : 0.740 8.301 39176 Z= 0.372 Chirality : 0.049 0.190 4600 Planarity : 0.006 0.054 4800 Dihedral : 17.956 176.266 4800 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.13 % Allowed : 20.42 % 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 aren not related in a simple way. whole: -1.18 (0.14), residues: 3528 helix: -0.07 (0.14), residues: 1344 sheet: -1.07 (0.28), residues: 232 loop : -1.25 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 182 TYR 0.010 0.002 TYR F 348 PHE 0.016 0.003 PHE C 90 HIS 0.005 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00618 (28800) covalent geometry : angle 0.74014 (39176) hydrogen bonds : bond 0.04780 ( 1110) hydrogen bonds : angle 5.80809 ( 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 564 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 443 time to evaluate : 1.037 Fit side-chains REVERT: A 327 CYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7944 (p) REVERT: A 450 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7417 (ttpt) REVERT: A 491 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6541 (tt0) REVERT: B 377 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7564 (mm) REVERT: B 450 LYS cc_start: 0.7800 (ttmm) cc_final: 0.7468 (ttpt) REVERT: B 491 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6556 (tt0) REVERT: C 450 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7448 (ttpt) REVERT: D 327 CYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8015 (p) REVERT: D 450 LYS cc_start: 0.7820 (ttmm) cc_final: 0.7410 (ttpt) REVERT: E 254 GLU cc_start: 0.7558 (tp30) cc_final: 0.7138 (tp30) REVERT: E 286 MET cc_start: 0.7895 (tpt) cc_final: 0.7576 (tpt) REVERT: E 450 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7391 (ttpt) REVERT: F 327 CYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7927 (p) REVERT: F 377 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7565 (mm) REVERT: F 450 LYS cc_start: 0.7776 (ttmm) cc_final: 0.7439 (ttpt) REVERT: G 450 LYS cc_start: 0.7782 (ttmm) cc_final: 0.7455 (ttpt) REVERT: H 327 CYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7992 (p) REVERT: H 450 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7357 (ttpt) REVERT: H 459 TYR cc_start: 0.7139 (t80) cc_final: 0.6806 (t80) REVERT: H 487 GLU cc_start: 0.7648 (mp0) cc_final: 0.7444 (mp0) outliers start: 121 outliers final: 92 residues processed: 537 average time/residue: 0.1642 time to fit residues: 145.9638 Evaluate side-chains 530 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 430 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 282 TYR Chi-restraints excluded: chain A residue 318 VAL 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 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 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 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 319 ASP Chi-restraints excluded: chain C residue 327 CYS 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 45 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 333 THR Chi-restraints excluded: chain D residue 370 VAL 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 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR 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 395 GLU 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 395 GLU 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 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 208 LYS Chi-restraints excluded: chain H residue 209 LEU 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 333 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU 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: 1.9990 chunk 231 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 55 optimal weight: 0.0270 chunk 130 optimal weight: 1.9990 chunk 318 optimal weight: 0.8980 chunk 24 optimal weight: 0.0040 chunk 284 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 overall best weight: 0.5050 ------------------------------------------------------------------------------- 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 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4530 r_free = 0.4530 target = 0.187040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.162119 restraints weight = 33660.733| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 1.69 r_work: 0.4148 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4026 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4080 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= 0.124 Angle : 0.619 7.753 39176 Z= 0.309 Chirality : 0.044 0.170 4600 Planarity : 0.005 0.066 4800 Dihedral : 17.321 178.874 4800 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.55 % Allowed : 21.65 % Favored : 74.80 % 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 aren not related in a simple way. whole: -0.60 (0.14), residues: 3528 helix: 0.55 (0.15), residues: 1344 sheet: -0.65 (0.25), residues: 280 loop : -1.05 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 182 TYR 0.013 0.001 TYR D 459 PHE 0.009 0.001 PHE E 24 HIS 0.002 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00296 (28800) covalent geometry : angle 0.61933 (39176) hydrogen bonds : bond 0.03598 ( 1110) hydrogen bonds : angle 5.36328 ( 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 531 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 427 time to evaluate : 1.190 Fit side-chains REVERT: A 450 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7386 (ttpt) REVERT: B 208 LYS cc_start: 0.4912 (mmmt) cc_final: 0.3920 (mttm) REVERT: B 377 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7258 (mm) REVERT: B 450 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7441 (ttpt) REVERT: C 450 LYS cc_start: 0.7784 (ttmm) cc_final: 0.7429 (ttpt) REVERT: D 271 ILE cc_start: 0.7465 (pp) cc_final: 0.7262 (pp) REVERT: D 283 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.6051 (mt0) REVERT: D 450 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7310 (ttpt) REVERT: E 450 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7428 (ttpt) REVERT: F 271 ILE cc_start: 0.7460 (pp) cc_final: 0.7253 (pp) REVERT: F 377 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7271 (mm) REVERT: F 450 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7434 (ttpt) REVERT: G 450 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7453 (ttpt) REVERT: H 271 ILE cc_start: 0.7468 (pp) cc_final: 0.7258 (pp) REVERT: H 283 GLN cc_start: 0.6461 (OUTLIER) cc_final: 0.6082 (mt0) REVERT: H 450 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7361 (ttpt) REVERT: H 459 TYR cc_start: 0.7200 (t80) cc_final: 0.6893 (t80) outliers start: 104 outliers final: 95 residues processed: 507 average time/residue: 0.1711 time to fit residues: 144.2428 Evaluate side-chains 511 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 412 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 318 VAL 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 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 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 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 45 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 114 PHE 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 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU 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 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 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 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 208 LYS 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 333 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU 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: 2.9990 chunk 315 optimal weight: 0.8980 chunk 336 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 230 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 223 optimal weight: 0.6980 chunk 345 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 466 HIS ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.189501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.162080 restraints weight = 33009.448| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.93 r_work: 0.4068 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3936 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28800 Z= 0.139 Angle : 0.622 8.405 39176 Z= 0.309 Chirality : 0.044 0.166 4600 Planarity : 0.005 0.063 4800 Dihedral : 16.836 179.739 4800 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.48 % Allowed : 21.65 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.14), residues: 3528 helix: 0.62 (0.15), residues: 1344 sheet: -0.53 (0.26), residues: 280 loop : -1.01 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 182 TYR 0.014 0.001 TYR E 459 PHE 0.009 0.001 PHE E 24 HIS 0.002 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00338 (28800) covalent geometry : angle 0.62175 (39176) hydrogen bonds : bond 0.03705 ( 1110) hydrogen bonds : angle 5.33637 ( 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 535 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 433 time to evaluate : 1.119 Fit side-chains REVERT: A 450 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7405 (ttpt) REVERT: B 377 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7392 (mm) REVERT: B 450 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7332 (ttpt) REVERT: B 491 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6231 (tt0) REVERT: C 450 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7399 (ttpt) REVERT: D 271 ILE cc_start: 0.7600 (pp) cc_final: 0.7355 (pp) REVERT: D 283 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6283 (mt0) REVERT: D 450 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7268 (ttpt) REVERT: E 450 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7353 (ttpt) REVERT: F 271 ILE cc_start: 0.7581 (pp) cc_final: 0.7377 (pp) REVERT: F 377 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7397 (mm) REVERT: F 450 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7358 (ttpt) REVERT: G 450 LYS cc_start: 0.7831 (ttmm) cc_final: 0.7369 (ttpt) REVERT: H 271 ILE cc_start: 0.7586 (pp) cc_final: 0.7338 (pp) REVERT: H 283 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.6303 (mt0) REVERT: H 450 LYS cc_start: 0.7668 (ttmm) cc_final: 0.7331 (ttpt) REVERT: H 459 TYR cc_start: 0.7201 (t80) cc_final: 0.6889 (t80) outliers start: 102 outliers final: 95 residues processed: 508 average time/residue: 0.1644 time to fit residues: 139.3297 Evaluate side-chains 524 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 424 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 318 VAL 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 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 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 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 319 ASP Chi-restraints excluded: chain C residue 327 CYS 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 45 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 45 ILE Chi-restraints excluded: chain E residue 114 PHE 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 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU 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 395 GLU 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 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 158 VAL 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 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 208 LYS 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 395 GLU 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: 0.7980 chunk 306 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 354 optimal weight: 0.9980 chunk 318 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 307 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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** H 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.189345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.162487 restraints weight = 33267.790| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 1.92 r_work: 0.4155 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28800 Z= 0.115 Angle : 0.600 8.750 39176 Z= 0.296 Chirality : 0.043 0.181 4600 Planarity : 0.005 0.067 4800 Dihedral : 15.943 179.871 4800 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.97 % Allowed : 22.37 % Favored : 74.66 % 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 aren not related in a simple way. whole: -0.49 (0.14), residues: 3528 helix: 0.65 (0.15), residues: 1384 sheet: -0.39 (0.27), residues: 264 loop : -1.05 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 259 TYR 0.009 0.001 TYR G 258 PHE 0.008 0.001 PHE E 24 HIS 0.002 0.000 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.00272 (28800) covalent geometry : angle 0.59979 (39176) hydrogen bonds : bond 0.03347 ( 1110) hydrogen bonds : angle 5.15364 ( 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 515 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 428 time to evaluate : 1.112 Fit side-chains REVERT: A 450 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7371 (ttpt) REVERT: B 208 LYS cc_start: 0.4818 (mmmt) cc_final: 0.3869 (mttm) REVERT: B 377 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7240 (mm) REVERT: B 450 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7342 (ttpt) REVERT: B 491 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6301 (tt0) REVERT: C 271 ILE cc_start: 0.7576 (pp) cc_final: 0.7357 (pp) REVERT: C 450 LYS cc_start: 0.7798 (ttmm) cc_final: 0.7340 (ttpt) REVERT: C 491 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6294 (tt0) REVERT: D 271 ILE cc_start: 0.7628 (pp) cc_final: 0.7423 (pp) REVERT: D 283 GLN cc_start: 0.6279 (OUTLIER) cc_final: 0.5906 (mt0) REVERT: D 450 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7315 (ttpt) REVERT: E 450 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7330 (ttpt) REVERT: F 377 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7241 (mm) REVERT: F 450 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7336 (ttpt) REVERT: G 450 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7330 (ttpt) REVERT: H 283 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5893 (mt0) REVERT: H 450 LYS cc_start: 0.7658 (ttmm) cc_final: 0.7172 (ttpt) REVERT: H 459 TYR cc_start: 0.7202 (t80) cc_final: 0.6897 (t80) outliers start: 87 outliers final: 79 residues processed: 486 average time/residue: 0.1615 time to fit residues: 130.9303 Evaluate side-chains 504 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 419 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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 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 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 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 491 GLU 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 327 CYS 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 45 ILE 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 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 E residue 45 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR 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 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 395 GLU 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 114 PHE Chi-restraints excluded: chain G residue 142 ILE 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 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 114 PHE 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 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU 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: 0.7980 chunk 95 optimal weight: 0.7980 chunk 300 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 333 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 316 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4548 r_free = 0.4548 target = 0.188564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.162417 restraints weight = 33520.142| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 1.86 r_work: 0.4151 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4022 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28800 Z= 0.135 Angle : 0.626 8.500 39176 Z= 0.308 Chirality : 0.044 0.177 4600 Planarity : 0.005 0.065 4800 Dihedral : 15.764 179.792 4800 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.31 % Allowed : 21.86 % Favored : 74.83 % 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 aren not related in a simple way. whole: -0.48 (0.14), residues: 3528 helix: 0.68 (0.15), residues: 1384 sheet: -0.37 (0.27), residues: 264 loop : -1.08 (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 B 294 PHE 0.009 0.001 PHE D 24 HIS 0.002 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00327 (28800) covalent geometry : angle 0.62582 (39176) hydrogen bonds : bond 0.03549 ( 1110) hydrogen bonds : angle 5.21038 ( 3114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7878.52 seconds wall clock time: 135 minutes 37.39 seconds (8137.39 seconds total)