Starting phenix.real_space_refine on Mon May 26 19:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7m_41986/05_2025/8u7m_41986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7m_41986/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7m_41986/05_2025/8u7m_41986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7m_41986/05_2025/8u7m_41986.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7m_41986/05_2025/8u7m_41986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7m_41986/05_2025/8u7m_41986.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.53, per 1000 atoms: 0.55 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: 7.11 Conformation dependent library (CDL) restraints added in 3.3 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6512 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 40 sheets defined 46.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 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: 10.29 Time building geometry restraints manager: 8.19 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: 0.04 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: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.440 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.300 ------------------------------------------------------------------------------- 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 : 10.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS D 372 PHE 0.013 0.002 PHE G 456 TYR 0.013 0.001 TYR E 459 ARG 0.009 0.001 ARG D 182 Details of bonding type rmsd hydrogen bonds : bond 0.14852 ( 1110) hydrogen bonds : angle 6.90590 ( 3114) covalent geometry : bond 0.00658 (28800) covalent geometry : angle 1.13481 (39176) *********************** 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 : 2.846 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 outliers start: 8 outliers final: 0 residues processed: 507 average time/residue: 0.3517 time to fit residues: 292.3740 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 : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.0050 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 0.2980 chunk 210 optimal weight: 1.9990 chunk 326 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 C 469 GLN D 334 GLN D 368 GLN D 372 HIS E 334 GLN E 372 HIS E 469 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.195366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.168446 restraints weight = 32701.706| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 1.83 r_work: 0.4163 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4030 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28800 Z= 0.136 Angle : 0.656 7.310 39176 Z= 0.326 Chirality : 0.046 0.193 4600 Planarity : 0.005 0.064 4800 Dihedral : 20.894 155.564 4800 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.29 % Allowed : 15.78 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3528 helix: 0.36 (0.14), residues: 1360 sheet: -0.60 (0.32), residues: 240 loop : -0.96 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 93 PHE 0.021 0.002 PHE C 456 TYR 0.012 0.002 TYR E 289 ARG 0.007 0.000 ARG D 182 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 1110) hydrogen bonds : angle 5.54692 ( 3114) covalent geometry : bond 0.00315 (28800) covalent geometry : angle 0.65588 (39176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 473 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5722 (mpt-90) REVERT: A 182 ARG cc_start: 0.5881 (ttt-90) cc_final: 0.5540 (ttt-90) REVERT: A 208 LYS cc_start: 0.4593 (mmmt) cc_final: 0.3882 (mttm) REVERT: A 286 MET cc_start: 0.7991 (tpp) cc_final: 0.7741 (tpt) REVERT: A 353 TYR cc_start: 0.7210 (t80) cc_final: 0.6883 (t80) REVERT: A 450 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7155 (ttpt) REVERT: B 105 ARG cc_start: 0.6046 (OUTLIER) cc_final: 0.5827 (mpt-90) REVERT: B 179 MET cc_start: 0.7557 (ptt) cc_final: 0.7124 (ptt) REVERT: B 208 LYS cc_start: 0.4604 (mmmt) cc_final: 0.3869 (mttm) REVERT: B 450 LYS cc_start: 0.7698 (ttmm) cc_final: 0.7256 (ttpt) REVERT: C 105 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.5760 (mpt-90) REVERT: C 179 MET cc_start: 0.7575 (ptt) cc_final: 0.7112 (ptt) REVERT: C 450 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7048 (ttpt) REVERT: D 105 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5731 (mpt-90) REVERT: D 179 MET cc_start: 0.7647 (ptt) cc_final: 0.7209 (ptt) REVERT: D 182 ARG cc_start: 0.5738 (ttt-90) cc_final: 0.5297 (ttt-90) REVERT: D 353 TYR cc_start: 0.7224 (t80) cc_final: 0.6891 (t80) REVERT: D 450 LYS cc_start: 0.7623 (ttmm) cc_final: 0.6985 (ttpt) REVERT: E 105 ARG cc_start: 0.5948 (OUTLIER) cc_final: 0.3933 (tpt-90) REVERT: E 179 MET cc_start: 0.7577 (ptt) cc_final: 0.7133 (ptt) REVERT: E 182 ARG cc_start: 0.5801 (ttt-90) cc_final: 0.5388 (ttt-90) REVERT: E 286 MET cc_start: 0.7971 (tpp) cc_final: 0.7728 (tpt) REVERT: E 353 TYR cc_start: 0.7230 (t80) cc_final: 0.6902 (t80) REVERT: E 450 LYS cc_start: 0.7873 (ttmm) cc_final: 0.7187 (ttpt) REVERT: F 105 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5774 (mpt-90) REVERT: F 179 MET cc_start: 0.7501 (ptt) cc_final: 0.7075 (ptt) REVERT: F 353 TYR cc_start: 0.7229 (t80) cc_final: 0.6908 (t80) REVERT: F 450 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7067 (ttpt) REVERT: G 105 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5747 (mpt-90) REVERT: G 179 MET cc_start: 0.7540 (ptt) cc_final: 0.7133 (ptt) REVERT: G 450 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7065 (ttpt) REVERT: H 105 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.5750 (mpt-90) REVERT: H 179 MET cc_start: 0.7536 (ptt) cc_final: 0.7119 (ptt) REVERT: H 353 TYR cc_start: 0.7241 (t80) cc_final: 0.6902 (t80) REVERT: H 450 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7090 (ttpt) outliers start: 67 outliers final: 31 residues processed: 517 average time/residue: 0.3773 time to fit residues: 315.2277 Evaluate side-chains 453 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 414 time to evaluate : 3.120 ------------------------------------------------------------------------------- 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 A residue 282 TYR Chi-restraints excluded: chain A residue 327 CYS 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 209 LEU Chi-restraints excluded: chain C residue 333 THR 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 209 LEU Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 327 CYS 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 209 LEU Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 327 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 258 optimal weight: 0.3980 chunk 310 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 61 optimal weight: 0.0050 chunk 175 optimal weight: 0.9990 chunk 281 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 104 optimal weight: 0.0050 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 GLN E 469 GLN F 102 ASN G 469 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.198444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.172269 restraints weight = 32353.499| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 1.79 r_work: 0.4251 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4118 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28800 Z= 0.115 Angle : 0.585 6.542 39176 Z= 0.290 Chirality : 0.044 0.188 4600 Planarity : 0.004 0.051 4800 Dihedral : 19.457 150.858 4800 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.87 % Allowed : 16.67 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3528 helix: 0.69 (0.14), residues: 1360 sheet: -0.84 (0.31), residues: 224 loop : -0.77 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 92 PHE 0.014 0.002 PHE B 456 TYR 0.018 0.002 TYR B 459 ARG 0.005 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 1110) hydrogen bonds : angle 5.26588 ( 3114) covalent geometry : bond 0.00263 (28800) covalent geometry : angle 0.58504 (39176) *********************** 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 518 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 434 time to evaluate : 2.909 Fit side-chains REVERT: A 283 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.5668 (tt0) REVERT: A 353 TYR cc_start: 0.7223 (t80) cc_final: 0.6992 (t80) REVERT: A 450 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7371 (ttpt) REVERT: B 179 MET cc_start: 0.7412 (ptt) cc_final: 0.7010 (ptt) REVERT: B 208 LYS cc_start: 0.4544 (mmmt) cc_final: 0.3931 (mttm) REVERT: B 283 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.5628 (tt0) REVERT: B 450 LYS cc_start: 0.7486 (ttmm) cc_final: 0.7251 (ttpt) REVERT: C 179 MET cc_start: 0.7419 (ptt) cc_final: 0.7023 (ptt) REVERT: C 271 ILE cc_start: 0.7391 (pp) cc_final: 0.6988 (pp) REVERT: C 353 TYR cc_start: 0.7197 (t80) cc_final: 0.6871 (t80) REVERT: C 456 PHE cc_start: 0.8193 (t80) cc_final: 0.7582 (t80) REVERT: D 179 MET cc_start: 0.7486 (ptt) cc_final: 0.7024 (ptt) REVERT: D 182 ARG cc_start: 0.5923 (ttt-90) cc_final: 0.5542 (ttt-90) REVERT: D 271 ILE cc_start: 0.7293 (pp) cc_final: 0.6942 (pp) REVERT: D 450 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7335 (ttpt) REVERT: E 179 MET cc_start: 0.7420 (ptt) cc_final: 0.7020 (ptt) REVERT: E 283 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.5670 (tt0) REVERT: E 450 LYS cc_start: 0.7731 (ttmm) cc_final: 0.7327 (ttpt) REVERT: F 179 MET cc_start: 0.7446 (ptt) cc_final: 0.7036 (ptt) REVERT: F 271 ILE cc_start: 0.7339 (pp) cc_final: 0.7017 (pp) REVERT: F 283 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.5605 (tt0) REVERT: F 456 PHE cc_start: 0.8164 (t80) cc_final: 0.7532 (t80) REVERT: G 179 MET cc_start: 0.7398 (ptt) cc_final: 0.7026 (ptt) REVERT: G 271 ILE cc_start: 0.7159 (pp) cc_final: 0.6888 (pp) REVERT: G 456 PHE cc_start: 0.8161 (t80) cc_final: 0.7555 (t80) REVERT: H 179 MET cc_start: 0.7397 (ptt) cc_final: 0.6993 (ptt) REVERT: H 182 ARG cc_start: 0.5810 (ttt-90) cc_final: 0.5586 (tmt-80) REVERT: H 450 LYS cc_start: 0.7549 (ttmm) cc_final: 0.7164 (ttpt) outliers start: 84 outliers final: 46 residues processed: 498 average time/residue: 0.3609 time to fit residues: 293.3633 Evaluate side-chains 448 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 398 time to evaluate : 2.879 ------------------------------------------------------------------------------- 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 283 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 94 ASN 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 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 321 optimal weight: 2.9990 chunk 45 optimal weight: 0.0040 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 335 optimal weight: 0.6980 chunk 68 optimal weight: 0.0970 chunk 144 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 274 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 368 GLN B 102 ASN B 368 GLN C 102 ASN C 469 GLN D 102 ASN D 368 GLN E 102 ASN G 102 ASN H 102 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.196500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.169905 restraints weight = 32965.863| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 1.87 r_work: 0.4240 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4114 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28800 Z= 0.107 Angle : 0.559 7.746 39176 Z= 0.276 Chirality : 0.042 0.157 4600 Planarity : 0.004 0.044 4800 Dihedral : 18.556 164.831 4800 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.35 % Allowed : 16.56 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3528 helix: 0.84 (0.15), residues: 1384 sheet: -0.13 (0.27), residues: 280 loop : -0.76 (0.15), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 92 PHE 0.015 0.001 PHE B 456 TYR 0.008 0.001 TYR A 282 ARG 0.003 0.000 ARG D 182 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 1110) hydrogen bonds : angle 5.11539 ( 3114) covalent geometry : bond 0.00245 (28800) covalent geometry : angle 0.55862 (39176) *********************** 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 514 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 416 time to evaluate : 3.047 Fit side-chains revert: symmetry clash REVERT: A 271 ILE cc_start: 0.7399 (pp) cc_final: 0.7081 (pp) REVERT: A 283 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5566 (tt0) REVERT: A 286 MET cc_start: 0.7974 (tpp) cc_final: 0.7707 (tpt) REVERT: A 450 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7357 (ttpt) REVERT: B 179 MET cc_start: 0.7330 (ptt) cc_final: 0.7101 (ptt) REVERT: B 208 LYS cc_start: 0.4506 (mmmt) cc_final: 0.3799 (mttm) REVERT: B 271 ILE cc_start: 0.7384 (pp) cc_final: 0.7074 (pp) REVERT: B 283 GLN cc_start: 0.6283 (OUTLIER) cc_final: 0.5513 (tt0) REVERT: B 450 LYS cc_start: 0.7557 (ttmm) cc_final: 0.7300 (ttpt) REVERT: C 150 MET cc_start: 0.6343 (tpt) cc_final: 0.5777 (tpt) REVERT: C 179 MET cc_start: 0.7341 (ptt) cc_final: 0.7105 (ptt) REVERT: C 271 ILE cc_start: 0.7216 (pp) cc_final: 0.6961 (pp) REVERT: C 283 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.5643 (tt0) REVERT: C 456 PHE cc_start: 0.8218 (t80) cc_final: 0.7650 (t80) REVERT: D 150 MET cc_start: 0.6344 (tpt) cc_final: 0.5770 (tpt) REVERT: D 179 MET cc_start: 0.7357 (ptt) cc_final: 0.7050 (ptt) REVERT: D 182 ARG cc_start: 0.5771 (ttt-90) cc_final: 0.5487 (tmt-80) REVERT: D 271 ILE cc_start: 0.7262 (pp) cc_final: 0.6950 (pp) REVERT: D 283 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.5951 (tt0) REVERT: D 450 LYS cc_start: 0.7706 (ttmm) cc_final: 0.7326 (ttpt) REVERT: E 179 MET cc_start: 0.7349 (ptt) cc_final: 0.7109 (ptt) REVERT: E 271 ILE cc_start: 0.7297 (pp) cc_final: 0.6933 (pp) REVERT: E 283 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.5599 (tt0) REVERT: E 286 MET cc_start: 0.8028 (tpp) cc_final: 0.7747 (tpt) REVERT: E 450 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7282 (ttpt) REVERT: F 150 MET cc_start: 0.6418 (tpt) cc_final: 0.5820 (tpt) REVERT: F 179 MET cc_start: 0.7444 (ptt) cc_final: 0.7165 (ptt) REVERT: F 271 ILE cc_start: 0.7283 (pp) cc_final: 0.6968 (pp) REVERT: F 283 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.5492 (tt0) REVERT: F 377 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7151 (mm) REVERT: F 456 PHE cc_start: 0.8195 (t80) cc_final: 0.7579 (t80) REVERT: G 179 MET cc_start: 0.7336 (ptt) cc_final: 0.7082 (ptt) REVERT: G 271 ILE cc_start: 0.7413 (pp) cc_final: 0.7184 (pp) REVERT: G 456 PHE cc_start: 0.8199 (t80) cc_final: 0.7621 (t80) REVERT: H 150 MET cc_start: 0.6376 (tpt) cc_final: 0.5823 (tpt) REVERT: H 179 MET cc_start: 0.7316 (ptt) cc_final: 0.7048 (ptt) REVERT: H 271 ILE cc_start: 0.7274 (pp) cc_final: 0.6977 (pp) REVERT: H 283 GLN cc_start: 0.6283 (OUTLIER) cc_final: 0.5939 (tt0) REVERT: H 450 LYS cc_start: 0.7528 (ttmm) cc_final: 0.7173 (ttpt) outliers start: 98 outliers final: 63 residues processed: 479 average time/residue: 0.3345 time to fit residues: 271.3933 Evaluate side-chains 455 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 384 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 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 94 ASN Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE 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 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain 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 159 THR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 242 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 270 optimal weight: 0.6980 chunk 325 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 368 GLN B 230 ASN C 230 ASN D 230 ASN D 368 GLN E 230 ASN E 368 GLN F 230 ASN G 230 ASN G 469 GLN H 230 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.200206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.176714 restraints weight = 32521.434| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 1.53 r_work: 0.4286 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4164 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28800 Z= 0.143 Angle : 0.593 6.746 39176 Z= 0.296 Chirality : 0.045 0.170 4600 Planarity : 0.004 0.045 4800 Dihedral : 18.024 176.892 4800 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.76 % Allowed : 17.28 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3528 helix: 0.65 (0.14), residues: 1384 sheet: -0.41 (0.29), residues: 240 loop : -0.91 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 288 PHE 0.011 0.002 PHE B 456 TYR 0.009 0.002 TYR B 348 ARG 0.005 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 1110) hydrogen bonds : angle 5.23901 ( 3114) covalent geometry : bond 0.00339 (28800) covalent geometry : angle 0.59270 (39176) *********************** 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 548 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 438 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4887 (mmmt) cc_final: 0.4053 (mttm) REVERT: A 283 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.6065 (mt0) REVERT: A 286 MET cc_start: 0.8007 (tpp) cc_final: 0.7778 (tpt) REVERT: A 450 LYS cc_start: 0.7691 (ttmm) cc_final: 0.7394 (ttpt) REVERT: A 491 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6110 (tt0) REVERT: B 208 LYS cc_start: 0.4870 (mmmt) cc_final: 0.4078 (mttm) REVERT: B 377 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7221 (mm) REVERT: B 491 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6020 (tt0) REVERT: C 208 LYS cc_start: 0.4855 (mmmt) cc_final: 0.4023 (mttm) REVERT: C 271 ILE cc_start: 0.7282 (pp) cc_final: 0.6927 (pp) REVERT: D 208 LYS cc_start: 0.4854 (mmmt) cc_final: 0.4070 (mttm) REVERT: D 283 GLN cc_start: 0.6344 (OUTLIER) cc_final: 0.5741 (tt0) REVERT: D 450 LYS cc_start: 0.7678 (ttmm) cc_final: 0.7401 (ttpt) REVERT: E 208 LYS cc_start: 0.4839 (mmmt) cc_final: 0.4051 (mttm) REVERT: E 271 ILE cc_start: 0.7317 (pp) cc_final: 0.6984 (pp) REVERT: E 283 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.6112 (mt0) REVERT: E 450 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7385 (ttpt) REVERT: F 208 LYS cc_start: 0.4877 (mmmt) cc_final: 0.4067 (mttm) REVERT: F 271 ILE cc_start: 0.7301 (pp) cc_final: 0.7012 (pp) REVERT: F 377 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7253 (mm) REVERT: G 271 ILE cc_start: 0.7340 (pp) cc_final: 0.7109 (pp) REVERT: H 283 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.5699 (tt0) REVERT: H 450 LYS cc_start: 0.7610 (ttmm) cc_final: 0.7380 (ttpt) outliers start: 110 outliers final: 82 residues processed: 526 average time/residue: 0.3457 time to fit residues: 299.9260 Evaluate side-chains 505 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 415 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 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 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 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 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 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 260 LEU 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 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 128 optimal weight: 0.0050 chunk 160 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 340 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 353 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 139 optimal weight: 0.0670 chunk 333 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.202703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.177739 restraints weight = 32341.763| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 1.72 r_work: 0.4294 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4163 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 28800 Z= 0.109 Angle : 0.558 7.528 39176 Z= 0.277 Chirality : 0.043 0.165 4600 Planarity : 0.004 0.050 4800 Dihedral : 17.656 176.883 4800 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.65 % Allowed : 18.95 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3528 helix: 0.84 (0.14), residues: 1384 sheet: -0.16 (0.27), residues: 264 loop : -0.87 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 125 PHE 0.015 0.001 PHE B 456 TYR 0.009 0.001 TYR E 289 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 1110) hydrogen bonds : angle 5.05848 ( 3114) covalent geometry : bond 0.00253 (28800) covalent geometry : angle 0.55776 (39176) *********************** 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 539 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 432 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4860 (mmmt) cc_final: 0.3987 (mttm) REVERT: A 283 GLN cc_start: 0.6326 (OUTLIER) cc_final: 0.5652 (tt0) REVERT: A 450 LYS cc_start: 0.7693 (ttmm) cc_final: 0.7382 (ttpt) REVERT: A 459 TYR cc_start: 0.6967 (t80) cc_final: 0.6756 (t80) REVERT: B 208 LYS cc_start: 0.4857 (mmmt) cc_final: 0.4018 (mttm) REVERT: B 271 ILE cc_start: 0.7417 (pp) cc_final: 0.7154 (pp) REVERT: B 283 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5466 (tt0) REVERT: B 377 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7167 (mm) REVERT: C 208 LYS cc_start: 0.4817 (mmmt) cc_final: 0.3967 (mttm) REVERT: C 271 ILE cc_start: 0.7258 (pp) cc_final: 0.7034 (pp) REVERT: C 283 GLN cc_start: 0.6236 (OUTLIER) cc_final: 0.5563 (tt0) REVERT: D 150 MET cc_start: 0.6464 (tpt) cc_final: 0.5828 (tpt) REVERT: D 208 LYS cc_start: 0.4894 (mmmt) cc_final: 0.3951 (mttm) REVERT: D 271 ILE cc_start: 0.7339 (pp) cc_final: 0.7102 (pp) REVERT: D 283 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5511 (tt0) REVERT: D 450 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7347 (ttpt) REVERT: E 208 LYS cc_start: 0.4764 (mmmt) cc_final: 0.3938 (mttm) REVERT: E 271 ILE cc_start: 0.7330 (pp) cc_final: 0.7072 (pp) REVERT: E 283 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.5821 (mt0) REVERT: E 450 LYS cc_start: 0.7756 (ttmm) cc_final: 0.7441 (ttpt) REVERT: E 459 TYR cc_start: 0.6972 (t80) cc_final: 0.6751 (t80) REVERT: F 150 MET cc_start: 0.6505 (tpt) cc_final: 0.5862 (tpt) REVERT: F 208 LYS cc_start: 0.4853 (mmmt) cc_final: 0.4000 (mttm) REVERT: F 271 ILE cc_start: 0.7357 (pp) cc_final: 0.7113 (pp) REVERT: F 283 GLN cc_start: 0.6187 (OUTLIER) cc_final: 0.5443 (tt0) REVERT: F 377 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7170 (mm) REVERT: G 283 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.5922 (mt0) REVERT: H 271 ILE cc_start: 0.7336 (pp) cc_final: 0.7047 (pp) REVERT: H 283 GLN cc_start: 0.6225 (OUTLIER) cc_final: 0.5544 (tt0) REVERT: H 450 LYS cc_start: 0.7716 (ttmm) cc_final: 0.7408 (ttpt) outliers start: 107 outliers final: 85 residues processed: 517 average time/residue: 0.3622 time to fit residues: 309.5085 Evaluate side-chains 511 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 416 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU 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 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 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 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 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain 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 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 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 260 LEU Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 317 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 135 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.199869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.176718 restraints weight = 32424.777| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 1.51 r_work: 0.4287 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28800 Z= 0.134 Angle : 0.593 7.864 39176 Z= 0.295 Chirality : 0.044 0.172 4600 Planarity : 0.004 0.048 4800 Dihedral : 17.261 177.067 4800 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.89 % Allowed : 20.01 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3528 helix: 0.70 (0.14), residues: 1392 sheet: -0.56 (0.30), residues: 224 loop : -0.93 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 93 PHE 0.017 0.002 PHE C 35 TYR 0.008 0.001 TYR B 348 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1110) hydrogen bonds : angle 5.14040 ( 3114) covalent geometry : bond 0.00319 (28800) covalent geometry : angle 0.59256 (39176) *********************** 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 547 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 433 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.7747 (ptt) cc_final: 0.7454 (pmm) REVERT: A 208 LYS cc_start: 0.4888 (mmmt) cc_final: 0.4019 (mttm) REVERT: A 450 LYS cc_start: 0.7689 (ttmm) cc_final: 0.7337 (ttpt) REVERT: A 459 TYR cc_start: 0.7080 (t80) cc_final: 0.6813 (t80) REVERT: B 208 LYS cc_start: 0.4947 (mmmt) cc_final: 0.4086 (mttm) REVERT: B 271 ILE cc_start: 0.7306 (pp) cc_final: 0.7072 (pp) REVERT: B 283 GLN cc_start: 0.6276 (OUTLIER) cc_final: 0.5569 (tt0) REVERT: B 377 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7254 (mm) REVERT: B 491 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5996 (tt0) REVERT: C 208 LYS cc_start: 0.4917 (mmmt) cc_final: 0.4060 (mttm) REVERT: D 208 LYS cc_start: 0.4900 (mmmt) cc_final: 0.4041 (mttm) REVERT: D 271 ILE cc_start: 0.7351 (pp) cc_final: 0.7081 (pp) REVERT: D 283 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5621 (tt0) REVERT: D 450 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7397 (ttpt) REVERT: E 208 LYS cc_start: 0.4853 (mmmt) cc_final: 0.4018 (mttm) REVERT: E 450 LYS cc_start: 0.7688 (ttmm) cc_final: 0.7370 (ttpt) REVERT: E 459 TYR cc_start: 0.7091 (t80) cc_final: 0.6833 (t80) REVERT: F 208 LYS cc_start: 0.4881 (mmmt) cc_final: 0.4033 (mttm) REVERT: F 271 ILE cc_start: 0.7366 (pp) cc_final: 0.7127 (pp) REVERT: F 283 GLN cc_start: 0.6248 (OUTLIER) cc_final: 0.5612 (mt0) REVERT: F 377 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7275 (mm) REVERT: G 283 GLN cc_start: 0.6268 (OUTLIER) cc_final: 0.5945 (mt0) REVERT: G 286 MET cc_start: 0.8011 (tpt) cc_final: 0.7771 (tpt) REVERT: H 271 ILE cc_start: 0.7384 (pp) cc_final: 0.7145 (pp) REVERT: H 283 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5642 (tt0) REVERT: H 450 LYS cc_start: 0.7704 (ttmm) cc_final: 0.7417 (ttpt) outliers start: 114 outliers final: 83 residues processed: 527 average time/residue: 0.3473 time to fit residues: 304.1661 Evaluate side-chains 505 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 414 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 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 453 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 229 optimal weight: 0.7980 chunk 341 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4633 r_free = 0.4633 target = 0.198457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.174685 restraints weight = 32672.608| |-----------------------------------------------------------------------------| r_work (start): 0.4394 rms_B_bonded: 1.61 r_work: 0.4256 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28800 Z= 0.141 Angle : 0.605 7.953 39176 Z= 0.302 Chirality : 0.044 0.163 4600 Planarity : 0.004 0.055 4800 Dihedral : 16.903 178.626 4800 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.69 % Allowed : 20.56 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3528 helix: 0.62 (0.14), residues: 1392 sheet: -0.14 (0.26), residues: 280 loop : -1.00 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 93 PHE 0.020 0.002 PHE F 35 TYR 0.008 0.001 TYR G 459 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 1110) hydrogen bonds : angle 5.15968 ( 3114) covalent geometry : bond 0.00335 (28800) covalent geometry : angle 0.60470 (39176) *********************** 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 543 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 435 time to evaluate : 2.925 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4933 (mmmt) cc_final: 0.4030 (mttm) REVERT: A 450 LYS cc_start: 0.7802 (ttmm) cc_final: 0.7400 (ttpt) REVERT: A 459 TYR cc_start: 0.7192 (t80) cc_final: 0.6914 (t80) REVERT: A 491 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6158 (tt0) REVERT: B 208 LYS cc_start: 0.4958 (mmmt) cc_final: 0.4088 (mttm) REVERT: B 283 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5692 (mt0) REVERT: B 377 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7213 (mm) REVERT: B 491 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6292 (tt0) REVERT: C 208 LYS cc_start: 0.4922 (mmmt) cc_final: 0.4067 (mttm) REVERT: D 208 LYS cc_start: 0.5070 (mmmt) cc_final: 0.4037 (mttm) REVERT: D 271 ILE cc_start: 0.7386 (pp) cc_final: 0.7108 (pp) REVERT: D 283 GLN cc_start: 0.6230 (OUTLIER) cc_final: 0.5625 (tt0) REVERT: D 450 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7390 (ttpt) REVERT: E 208 LYS cc_start: 0.4915 (mmmt) cc_final: 0.4042 (mttm) REVERT: E 450 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7359 (ttpt) REVERT: E 459 TYR cc_start: 0.7202 (t80) cc_final: 0.6928 (t80) REVERT: F 208 LYS cc_start: 0.4916 (mmmt) cc_final: 0.4043 (mttm) REVERT: F 271 ILE cc_start: 0.7406 (pp) cc_final: 0.7157 (pp) REVERT: F 283 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5617 (mt0) REVERT: F 377 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7227 (mm) REVERT: H 271 ILE cc_start: 0.7424 (pp) cc_final: 0.7173 (pp) REVERT: H 283 GLN cc_start: 0.6302 (OUTLIER) cc_final: 0.5686 (tt0) REVERT: H 450 LYS cc_start: 0.7563 (ttmm) cc_final: 0.7328 (ttpt) outliers start: 108 outliers final: 92 residues processed: 521 average time/residue: 0.3509 time to fit residues: 304.4400 Evaluate side-chains 527 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 427 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU 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 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 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 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 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 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 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 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 94 ASN Chi-restraints excluded: chain H residue 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 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 290 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 355 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 223 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ** 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 = 0.4455 r_free = 0.4455 target = 0.186690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.158834 restraints weight = 33230.672| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.96 r_work: 0.4041 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28800 Z= 0.204 Angle : 0.675 7.777 39176 Z= 0.339 Chirality : 0.047 0.164 4600 Planarity : 0.005 0.059 4800 Dihedral : 16.669 179.863 4800 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.59 % Allowed : 21.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3528 helix: 0.33 (0.14), residues: 1344 sheet: -0.59 (0.29), residues: 240 loop : -0.97 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 92 PHE 0.024 0.002 PHE F 35 TYR 0.011 0.002 TYR G 459 ARG 0.004 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1110) hydrogen bonds : angle 5.51881 ( 3114) covalent geometry : bond 0.00492 (28800) covalent geometry : angle 0.67486 (39176) *********************** 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 546 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 441 time to evaluate : 2.910 Fit side-chains REVERT: A 179 MET cc_start: 0.7715 (ptt) cc_final: 0.7419 (pmm) REVERT: A 208 LYS cc_start: 0.5044 (mmmt) cc_final: 0.3854 (mttm) REVERT: A 450 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7287 (ttpt) REVERT: A 491 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: B 208 LYS cc_start: 0.4991 (mmmt) cc_final: 0.3819 (mttm) REVERT: B 377 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7425 (mm) REVERT: D 208 LYS cc_start: 0.5015 (mmmt) cc_final: 0.3833 (mttm) REVERT: D 254 GLU cc_start: 0.7603 (tp30) cc_final: 0.7399 (tp30) REVERT: D 450 LYS cc_start: 0.7779 (ttmm) cc_final: 0.7381 (ttpt) REVERT: D 491 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6579 (tt0) REVERT: E 208 LYS cc_start: 0.5089 (mmmt) cc_final: 0.3831 (mttm) REVERT: E 450 LYS cc_start: 0.7873 (ttmm) cc_final: 0.7387 (ttpt) REVERT: F 377 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7425 (mm) REVERT: G 327 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7961 (p) REVERT: H 327 CYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8044 (p) REVERT: H 450 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7313 (ttpt) outliers start: 105 outliers final: 86 residues processed: 528 average time/residue: 0.3382 time to fit residues: 294.9656 Evaluate side-chains 512 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 420 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU 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 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 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 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 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 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS 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 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 208 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 328 optimal weight: 0.3980 chunk 81 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.188338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.160671 restraints weight = 33598.244| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 1.97 r_work: 0.4146 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28800 Z= 0.122 Angle : 0.607 7.604 39176 Z= 0.301 Chirality : 0.043 0.179 4600 Planarity : 0.004 0.065 4800 Dihedral : 16.076 179.983 4800 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.21 % Allowed : 22.34 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3528 helix: 0.54 (0.14), residues: 1392 sheet: -0.45 (0.27), residues: 264 loop : -1.03 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 92 PHE 0.021 0.002 PHE F 35 TYR 0.010 0.001 TYR C 258 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 1110) hydrogen bonds : angle 5.18902 ( 3114) covalent geometry : bond 0.00287 (28800) covalent geometry : angle 0.60735 (39176) ********************** 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 521 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 427 time to evaluate : 3.339 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4960 (mmmt) cc_final: 0.3791 (mttm) REVERT: A 450 LYS cc_start: 0.7866 (ttmm) cc_final: 0.7325 (ttpt) REVERT: B 70 MET cc_start: 0.7841 (mtp) cc_final: 0.7515 (mtp) REVERT: B 208 LYS cc_start: 0.4868 (mmmt) cc_final: 0.3853 (mttm) REVERT: B 377 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7247 (mm) REVERT: B 461 ILE cc_start: 0.6024 (mm) cc_final: 0.5776 (tp) REVERT: B 491 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6519 (tt0) REVERT: C 217 GLU cc_start: 0.5477 (mp0) cc_final: 0.5044 (pp20) REVERT: C 491 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6574 (tt0) REVERT: D 208 LYS cc_start: 0.4995 (mmmt) cc_final: 0.3833 (mttm) REVERT: D 271 ILE cc_start: 0.7571 (pp) cc_final: 0.7291 (pp) REVERT: D 450 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7331 (ttpt) REVERT: E 208 LYS cc_start: 0.4995 (mmmt) cc_final: 0.3810 (mttm) REVERT: E 450 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7296 (ttpt) REVERT: E 491 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6535 (tt0) REVERT: F 208 LYS cc_start: 0.4995 (mmmt) cc_final: 0.3863 (mttm) REVERT: F 271 ILE cc_start: 0.7565 (pp) cc_final: 0.7337 (pp) REVERT: F 377 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7258 (mm) REVERT: H 166 LEU cc_start: 0.6693 (mp) cc_final: 0.5910 (mt) REVERT: H 271 ILE cc_start: 0.7567 (pp) cc_final: 0.7286 (pp) REVERT: H 450 LYS cc_start: 0.7643 (ttmm) cc_final: 0.7261 (ttpt) REVERT: H 459 TYR cc_start: 0.7063 (t80) cc_final: 0.6743 (t80) outliers start: 94 outliers final: 84 residues processed: 500 average time/residue: 0.3463 time to fit residues: 288.1022 Evaluate side-chains 511 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 422 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 257 LYS 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 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU 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 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 476 LEU Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 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 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS 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 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 109 optimal weight: 1.9990 chunk 308 optimal weight: 8.9990 chunk 192 optimal weight: 0.3980 chunk 345 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 231 optimal weight: 0.0970 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.190063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.162294 restraints weight = 32783.368| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.95 r_work: 0.4079 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28800 Z= 0.148 Angle : 0.632 8.247 39176 Z= 0.312 Chirality : 0.045 0.183 4600 Planarity : 0.005 0.062 4800 Dihedral : 15.987 180.000 4800 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.45 % Allowed : 21.93 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3528 helix: 0.65 (0.14), residues: 1352 sheet: -0.32 (0.26), residues: 280 loop : -0.89 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 93 PHE 0.024 0.002 PHE C 35 TYR 0.010 0.001 TYR C 459 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1110) hydrogen bonds : angle 5.27037 ( 3114) covalent geometry : bond 0.00357 (28800) covalent geometry : angle 0.63163 (39176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16016.96 seconds wall clock time: 277 minutes 32.04 seconds (16652.04 seconds total)