Starting phenix.real_space_refine on Tue Jun 24 17:14:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7m_41986/06_2025/8u7m_41986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7m_41986/06_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_41986/06_2025/8u7m_41986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7m_41986/06_2025/8u7m_41986.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7m_41986/06_2025/8u7m_41986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7m_41986/06_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-5710/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: 16.30, per 1000 atoms: 0.58 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: 7.31 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: 3.43 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: 10.38 Time building geometry restraints manager: 8.54 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: 0.03 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 62.900 Find NCS groups from input model: 1.240 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.130 ------------------------------------------------------------------------------- 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 : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 507 average time/residue: 0.3636 time to fit residues: 301.5638 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 : 2.968 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 372 HIS B 334 GLN B 372 HIS C 334 GLN C 372 HIS D 334 GLN D 368 GLN D 372 HIS E 334 GLN E 372 HIS F 334 GLN F 372 HIS G 334 GLN G 372 HIS H 334 GLN H 372 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.196121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.169199 restraints weight = 32656.294| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 1.82 r_work: 0.4221 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4092 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28800 Z= 0.133 Angle : 0.654 7.396 39176 Z= 0.324 Chirality : 0.045 0.184 4600 Planarity : 0.005 0.065 4800 Dihedral : 21.029 155.922 4800 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.29 % Allowed : 15.44 % Favored : 82.27 % 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: -0.60 (0.14), residues: 3528 helix: 0.39 (0.14), residues: 1360 sheet: -0.58 (0.32), residues: 240 loop : -0.93 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 125 PHE 0.020 0.002 PHE C 456 TYR 0.013 0.001 TYR A 289 ARG 0.007 0.000 ARG D 182 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 1110) hydrogen bonds : angle 5.57557 ( 3114) covalent geometry : bond 0.00309 (28800) covalent geometry : angle 0.65367 (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 545 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 478 time to evaluate : 2.729 Fit side-chains REVERT: A 105 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5703 (mpt-90) REVERT: A 182 ARG cc_start: 0.5776 (ttt-90) cc_final: 0.5424 (ttt-90) REVERT: A 286 MET cc_start: 0.8022 (tpp) cc_final: 0.7818 (tpt) REVERT: A 353 TYR cc_start: 0.7188 (t80) cc_final: 0.6864 (t80) REVERT: A 450 LYS cc_start: 0.7869 (ttmm) cc_final: 0.7227 (ttpt) REVERT: B 179 MET cc_start: 0.7531 (ptt) cc_final: 0.7102 (ptt) REVERT: B 208 LYS cc_start: 0.4639 (mmmt) cc_final: 0.4022 (mttm) REVERT: B 450 LYS cc_start: 0.7686 (ttmm) cc_final: 0.7291 (ttpt) REVERT: C 105 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.5741 (mpt-90) REVERT: C 179 MET cc_start: 0.7547 (ptt) cc_final: 0.7089 (ptt) REVERT: C 182 ARG cc_start: 0.5821 (ttt-90) cc_final: 0.5282 (ttt-90) REVERT: C 450 LYS cc_start: 0.7645 (ttmm) cc_final: 0.7265 (ttpt) REVERT: D 105 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5717 (mpt-90) REVERT: D 179 MET cc_start: 0.7561 (ptt) cc_final: 0.7097 (ptt) REVERT: D 182 ARG cc_start: 0.5830 (ttt-90) cc_final: 0.5389 (ttt-90) REVERT: D 353 TYR cc_start: 0.7196 (t80) cc_final: 0.6868 (t80) REVERT: D 450 LYS cc_start: 0.7597 (ttmm) cc_final: 0.7212 (ttpt) REVERT: E 105 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.5716 (mpt-90) REVERT: E 179 MET cc_start: 0.7517 (ptt) cc_final: 0.7094 (ptt) REVERT: E 182 ARG cc_start: 0.5771 (ttt-90) cc_final: 0.5357 (ttt-90) REVERT: E 353 TYR cc_start: 0.7208 (t80) cc_final: 0.6891 (t80) REVERT: E 450 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7198 (ttpt) REVERT: F 105 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5755 (mpt-90) REVERT: F 179 MET cc_start: 0.7473 (ptt) cc_final: 0.7059 (ptt) REVERT: F 353 TYR cc_start: 0.7209 (t80) cc_final: 0.6889 (t80) REVERT: F 450 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7280 (ttpt) REVERT: G 105 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5734 (mpt-90) REVERT: G 179 MET cc_start: 0.7508 (ptt) cc_final: 0.7077 (ptt) REVERT: G 450 LYS cc_start: 0.7658 (ttmm) cc_final: 0.7268 (ttpt) REVERT: H 105 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.5733 (mpt-90) REVERT: H 179 MET cc_start: 0.7505 (ptt) cc_final: 0.7095 (ptt) REVERT: H 353 TYR cc_start: 0.7215 (t80) cc_final: 0.6890 (t80) REVERT: H 450 LYS cc_start: 0.7706 (ttmm) cc_final: 0.7076 (ttpt) outliers start: 67 outliers final: 32 residues processed: 522 average time/residue: 0.3875 time to fit residues: 329.2840 Evaluate side-chains 477 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 438 time to evaluate : 2.825 ------------------------------------------------------------------------------- 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 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 283 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain 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: 0.7980 chunk 310 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 281 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.194431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.167826 restraints weight = 32651.765| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 1.82 r_work: 0.4151 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4021 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28800 Z= 0.135 Angle : 0.613 6.439 39176 Z= 0.305 Chirality : 0.045 0.190 4600 Planarity : 0.004 0.051 4800 Dihedral : 19.361 148.797 4800 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.79 % Allowed : 15.44 % Favored : 80.77 % 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: -0.48 (0.14), residues: 3528 helix: 0.57 (0.14), residues: 1352 sheet: -0.85 (0.32), residues: 224 loop : -0.87 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 288 PHE 0.019 0.002 PHE E 35 TYR 0.019 0.002 TYR H 459 ARG 0.006 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 1110) hydrogen bonds : angle 5.33929 ( 3114) covalent geometry : bond 0.00321 (28800) covalent geometry : angle 0.61322 (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 565 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 454 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5801 (ttt-90) cc_final: 0.5600 (ttt-90) REVERT: A 208 LYS cc_start: 0.4745 (mmmt) cc_final: 0.3967 (mttm) REVERT: A 283 GLN cc_start: 0.6508 (OUTLIER) cc_final: 0.5745 (tt0) REVERT: A 286 MET cc_start: 0.8034 (tpp) cc_final: 0.7778 (tpt) REVERT: B 179 MET cc_start: 0.7427 (ptt) cc_final: 0.6995 (ptt) REVERT: B 208 LYS cc_start: 0.4713 (mmmt) cc_final: 0.3946 (mttm) REVERT: B 283 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.5751 (tt0) REVERT: B 450 LYS cc_start: 0.7519 (ttmm) cc_final: 0.7294 (ttpt) REVERT: C 179 MET cc_start: 0.7423 (ptt) cc_final: 0.7011 (ptt) REVERT: C 182 ARG cc_start: 0.5851 (ttt-90) cc_final: 0.5591 (ttt-90) REVERT: C 208 LYS cc_start: 0.4772 (mmmt) cc_final: 0.4003 (mttm) REVERT: C 271 ILE cc_start: 0.7425 (pp) cc_final: 0.7017 (pp) REVERT: D 179 MET cc_start: 0.7502 (ptt) cc_final: 0.7041 (ptt) REVERT: D 208 LYS cc_start: 0.4923 (mmmt) cc_final: 0.4053 (mttm) REVERT: D 283 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.5861 (tt0) REVERT: D 450 LYS cc_start: 0.7535 (ttmm) cc_final: 0.7259 (ttpt) REVERT: E 179 MET cc_start: 0.7423 (ptt) cc_final: 0.7019 (ptt) REVERT: E 208 LYS cc_start: 0.4804 (mmmt) cc_final: 0.3957 (mttm) REVERT: E 283 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.5761 (tt0) REVERT: E 450 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7342 (ttpt) REVERT: F 179 MET cc_start: 0.7532 (ptt) cc_final: 0.7095 (ptt) REVERT: F 182 ARG cc_start: 0.5922 (ttt-90) cc_final: 0.5624 (ttt-90) REVERT: F 208 LYS cc_start: 0.4753 (mmmt) cc_final: 0.3988 (mttm) REVERT: F 283 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.5716 (tt0) REVERT: F 450 LYS cc_start: 0.7529 (ttmm) cc_final: 0.7306 (ttpt) REVERT: G 179 MET cc_start: 0.7407 (ptt) cc_final: 0.6980 (ptt) REVERT: G 271 ILE cc_start: 0.7279 (pp) cc_final: 0.6994 (pp) REVERT: G 450 LYS cc_start: 0.7523 (ttmm) cc_final: 0.7261 (ttpt) REVERT: H 179 MET cc_start: 0.7403 (ptt) cc_final: 0.6997 (ptt) REVERT: H 450 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7281 (ttpt) REVERT: H 459 TYR cc_start: 0.6613 (t80) cc_final: 0.6360 (t80) outliers start: 111 outliers final: 66 residues processed: 540 average time/residue: 0.3655 time to fit residues: 322.9234 Evaluate side-chains 497 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 426 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 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 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU 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 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 453 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 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 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 453 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 208 LYS 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 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 37 ILE 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 333 THR Chi-restraints excluded: chain H residue 367 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 321 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 335 optimal weight: 0.5980 chunk 68 optimal weight: 0.2980 chunk 144 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 274 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 368 GLN C 230 ASN D 368 GLN D 469 GLN E 368 GLN F 230 ASN F 368 GLN G 230 ASN G 368 GLN H 230 ASN H 368 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.196675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.173902 restraints weight = 32921.427| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 1.46 r_work: 0.4251 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2771 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= 0.162 Angle : 0.628 6.843 39176 Z= 0.314 Chirality : 0.045 0.162 4600 Planarity : 0.005 0.048 4800 Dihedral : 18.572 167.723 4800 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.17 % Allowed : 16.29 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.79 (0.14), residues: 3528 helix: 0.32 (0.14), residues: 1384 sheet: -0.90 (0.31), residues: 224 loop : -1.09 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 93 PHE 0.016 0.002 PHE C 456 TYR 0.008 0.002 TYR G 348 ARG 0.005 0.000 ARG E 182 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 1110) hydrogen bonds : angle 5.46025 ( 3114) covalent geometry : bond 0.00383 (28800) covalent geometry : angle 0.62822 (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 595 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 473 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4926 (mmmt) cc_final: 0.4073 (mttm) REVERT: A 286 MET cc_start: 0.8000 (tpp) cc_final: 0.7750 (tpt) REVERT: A 450 LYS cc_start: 0.7670 (ttmm) cc_final: 0.7349 (ttpt) REVERT: B 208 LYS cc_start: 0.4931 (mmmt) cc_final: 0.4125 (mttm) REVERT: B 491 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.5960 (tt0) REVERT: C 208 LYS cc_start: 0.4921 (mmmt) cc_final: 0.4084 (mttm) REVERT: C 491 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6051 (tt0) REVERT: D 179 MET cc_start: 0.7566 (ptt) cc_final: 0.7352 (ptt) REVERT: D 182 ARG cc_start: 0.6018 (ttt-90) cc_final: 0.5620 (tmt-80) REVERT: D 208 LYS cc_start: 0.5023 (mmmt) cc_final: 0.4072 (mttm) REVERT: D 456 PHE cc_start: 0.7692 (t80) cc_final: 0.7431 (t80) REVERT: E 208 LYS cc_start: 0.4873 (mmmt) cc_final: 0.4094 (mttm) REVERT: E 450 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7352 (ttpt) REVERT: E 459 TYR cc_start: 0.6931 (t80) cc_final: 0.6473 (t80) REVERT: F 208 LYS cc_start: 0.4931 (mmmt) cc_final: 0.4101 (mttm) REVERT: F 377 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7329 (mm) REVERT: G 182 ARG cc_start: 0.6008 (ttt-90) cc_final: 0.5558 (tmt-80) REVERT: G 491 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6021 (tt0) REVERT: H 136 ARG cc_start: 0.7335 (mmp-170) cc_final: 0.7124 (mmp-170) REVERT: H 182 ARG cc_start: 0.6023 (ttt-90) cc_final: 0.5578 (tmt-80) REVERT: H 450 LYS cc_start: 0.7608 (ttmm) cc_final: 0.7352 (ttpt) REVERT: H 491 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6015 (tt0) outliers start: 122 outliers final: 77 residues processed: 559 average time/residue: 0.3584 time to fit residues: 325.9214 Evaluate side-chains 511 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 429 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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 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 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU 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 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU 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 45 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 242 optimal weight: 0.4980 chunk 217 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 270 optimal weight: 0.2980 chunk 325 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 253 optimal weight: 0.1980 chunk 182 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN C 102 ASN D 102 ASN E 102 ASN F 102 ASN H 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.203461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.179997 restraints weight = 32240.702| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 1.60 r_work: 0.4320 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28800 Z= 0.100 Angle : 0.562 6.632 39176 Z= 0.279 Chirality : 0.043 0.154 4600 Planarity : 0.004 0.048 4800 Dihedral : 17.959 178.197 4800 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.53 % Allowed : 18.85 % Favored : 78.62 % 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: -0.29 (0.14), residues: 3528 helix: 0.79 (0.14), residues: 1384 sheet: -0.27 (0.28), residues: 264 loop : -0.92 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 92 PHE 0.015 0.001 PHE C 456 TYR 0.009 0.001 TYR E 282 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 1110) hydrogen bonds : angle 5.07252 ( 3114) covalent geometry : bond 0.00225 (28800) covalent geometry : angle 0.56207 (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 516 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 442 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4832 (mmmt) cc_final: 0.4021 (mttm) REVERT: A 271 ILE cc_start: 0.7339 (pp) cc_final: 0.7076 (pp) REVERT: A 283 GLN cc_start: 0.6092 (OUTLIER) cc_final: 0.5478 (tt0) REVERT: A 450 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7411 (ttpt) REVERT: A 459 TYR cc_start: 0.7044 (t80) cc_final: 0.6767 (t80) REVERT: B 208 LYS cc_start: 0.4746 (mmmt) cc_final: 0.3975 (mttm) REVERT: B 271 ILE cc_start: 0.7346 (pp) cc_final: 0.7036 (pp) REVERT: B 283 GLN cc_start: 0.6161 (OUTLIER) cc_final: 0.5473 (tt0) REVERT: B 377 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7051 (mm) REVERT: C 150 MET cc_start: 0.6484 (tpt) cc_final: 0.5789 (tpt) REVERT: C 208 LYS cc_start: 0.4799 (mmmt) cc_final: 0.3982 (mttm) REVERT: C 283 GLN cc_start: 0.6117 (OUTLIER) cc_final: 0.5718 (tt0) REVERT: D 150 MET cc_start: 0.6516 (tpt) cc_final: 0.5830 (tpt) REVERT: D 208 LYS cc_start: 0.4934 (mmmt) cc_final: 0.4059 (mttm) REVERT: D 271 ILE cc_start: 0.7284 (pp) cc_final: 0.7011 (pp) REVERT: D 283 GLN cc_start: 0.6174 (OUTLIER) cc_final: 0.5409 (tt0) REVERT: E 208 LYS cc_start: 0.4897 (mmmt) cc_final: 0.4031 (mttm) REVERT: E 271 ILE cc_start: 0.7290 (pp) cc_final: 0.7037 (pp) REVERT: E 283 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5552 (tt0) REVERT: E 450 LYS cc_start: 0.7718 (ttmm) cc_final: 0.7417 (ttpt) REVERT: E 459 TYR cc_start: 0.7024 (t80) cc_final: 0.6746 (t80) REVERT: F 208 LYS cc_start: 0.4865 (mmmt) cc_final: 0.4082 (mttm) REVERT: F 271 ILE cc_start: 0.7312 (pp) cc_final: 0.7103 (pp) REVERT: F 283 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.5389 (tt0) REVERT: F 377 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7166 (mm) REVERT: G 283 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5152 (tt0) REVERT: H 150 MET cc_start: 0.6503 (tpt) cc_final: 0.5831 (tpt) REVERT: H 271 ILE cc_start: 0.7312 (pp) cc_final: 0.7026 (pp) REVERT: H 283 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5695 (tt0) REVERT: H 450 LYS cc_start: 0.7569 (ttmm) cc_final: 0.7302 (ttpt) outliers start: 74 outliers final: 51 residues processed: 495 average time/residue: 0.3683 time to fit residues: 297.9891 Evaluate side-chains 483 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 422 time to evaluate : 3.165 ------------------------------------------------------------------------------- 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 283 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 370 VAL 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 476 LEU 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 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 370 VAL 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 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 383 THR Chi-restraints excluded: chain D residue 476 LEU 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 283 GLN 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 F residue 45 ILE 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 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 208 LYS 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 370 VAL Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain H residue 37 ILE 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 453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 128 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 340 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 353 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 ASN E 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.199753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.174646 restraints weight = 32589.614| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 1.76 r_work: 0.4266 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28800 Z= 0.126 Angle : 0.580 7.482 39176 Z= 0.288 Chirality : 0.044 0.174 4600 Planarity : 0.004 0.047 4800 Dihedral : 17.735 176.085 4800 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.93 % Allowed : 18.61 % Favored : 77.46 % 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: -0.35 (0.14), residues: 3528 helix: 0.80 (0.14), residues: 1384 sheet: -0.68 (0.30), residues: 224 loop : -0.94 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 93 PHE 0.019 0.002 PHE G 456 TYR 0.020 0.001 TYR F 459 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 1110) hydrogen bonds : angle 5.13251 ( 3114) covalent geometry : bond 0.00301 (28800) covalent geometry : angle 0.57965 (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 541 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 426 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.7617 (ptt) cc_final: 0.7038 (pmm) REVERT: A 208 LYS cc_start: 0.4884 (mmmt) cc_final: 0.3957 (mttm) REVERT: A 450 LYS cc_start: 0.7701 (ttmm) cc_final: 0.7368 (ttpt) REVERT: A 459 TYR cc_start: 0.7113 (t80) cc_final: 0.6823 (t80) REVERT: A 491 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6289 (tt0) REVERT: B 208 LYS cc_start: 0.4943 (mmmt) cc_final: 0.4040 (mttm) REVERT: B 271 ILE cc_start: 0.7446 (pp) cc_final: 0.7186 (pp) REVERT: B 283 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.5611 (tt0) REVERT: B 377 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7239 (mm) REVERT: B 450 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7507 (ttpt) REVERT: B 491 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.5974 (tt0) REVERT: C 208 LYS cc_start: 0.4833 (mmmt) cc_final: 0.3955 (mttm) REVERT: C 491 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6295 (tt0) REVERT: D 208 LYS cc_start: 0.4951 (mmmt) cc_final: 0.3956 (mttm) REVERT: D 271 ILE cc_start: 0.7445 (pp) cc_final: 0.7172 (pp) REVERT: D 283 GLN cc_start: 0.6225 (OUTLIER) cc_final: 0.5554 (tt0) REVERT: D 450 LYS cc_start: 0.7551 (ttpt) cc_final: 0.7292 (ttpt) REVERT: E 208 LYS cc_start: 0.4816 (mmmt) cc_final: 0.3970 (mttm) REVERT: E 450 LYS cc_start: 0.7662 (ttmm) cc_final: 0.7321 (ttpt) REVERT: E 459 TYR cc_start: 0.7165 (t80) cc_final: 0.6911 (t80) REVERT: F 208 LYS cc_start: 0.4912 (mmmt) cc_final: 0.3992 (mttm) REVERT: F 271 ILE cc_start: 0.7420 (pp) cc_final: 0.7208 (pp) REVERT: F 283 GLN cc_start: 0.6295 (OUTLIER) cc_final: 0.5620 (tt0) REVERT: G 283 GLN cc_start: 0.6225 (OUTLIER) cc_final: 0.5562 (tt0) REVERT: G 491 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6325 (tt0) REVERT: H 271 ILE cc_start: 0.7458 (pp) cc_final: 0.7177 (pp) REVERT: H 283 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5548 (tt0) REVERT: H 450 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7393 (ttpt) REVERT: H 491 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6207 (tt0) outliers start: 115 outliers final: 81 residues processed: 518 average time/residue: 0.3479 time to fit residues: 299.8767 Evaluate side-chains 499 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 407 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 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 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 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 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain 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 257 LYS Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain 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 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 317 optimal weight: 0.8980 chunk 278 optimal weight: 0.7980 chunk 201 optimal weight: 0.3980 chunk 179 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 340 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4653 r_free = 0.4653 target = 0.200159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.175110 restraints weight = 32363.402| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 1.76 r_work: 0.4267 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 28800 Z= 0.120 Angle : 0.583 7.782 39176 Z= 0.290 Chirality : 0.043 0.167 4600 Planarity : 0.004 0.053 4800 Dihedral : 17.366 176.549 4800 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.83 % Allowed : 19.36 % Favored : 76.81 % 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: -0.35 (0.14), residues: 3528 helix: 0.81 (0.14), residues: 1384 sheet: -0.30 (0.27), residues: 264 loop : -1.02 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 125 PHE 0.016 0.001 PHE B 456 TYR 0.010 0.001 TYR C 459 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 1110) hydrogen bonds : angle 5.08263 ( 3114) covalent geometry : bond 0.00282 (28800) covalent geometry : angle 0.58339 (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 546 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 434 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4877 (mmmt) cc_final: 0.3966 (mttm) REVERT: A 450 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7433 (ttpt) REVERT: A 459 TYR cc_start: 0.7169 (t80) cc_final: 0.6887 (t80) REVERT: A 491 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6114 (tt0) REVERT: B 208 LYS cc_start: 0.4942 (mmmt) cc_final: 0.4048 (mttm) REVERT: B 271 ILE cc_start: 0.7444 (pp) cc_final: 0.7195 (pp) REVERT: B 283 GLN cc_start: 0.6259 (OUTLIER) cc_final: 0.5585 (tt0) REVERT: B 377 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7172 (mm) REVERT: B 450 LYS cc_start: 0.7581 (ttpt) cc_final: 0.7218 (ttpt) REVERT: B 491 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6053 (tt0) REVERT: C 208 LYS cc_start: 0.4816 (mmmt) cc_final: 0.3949 (mttm) REVERT: C 283 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.5749 (tt0) REVERT: C 491 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6253 (tt0) REVERT: D 208 LYS cc_start: 0.4979 (mmmt) cc_final: 0.3937 (mttm) REVERT: D 271 ILE cc_start: 0.7433 (pp) cc_final: 0.7173 (pp) REVERT: D 283 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5626 (tt0) REVERT: E 208 LYS cc_start: 0.4858 (mmmt) cc_final: 0.4000 (mttm) REVERT: E 450 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7339 (ttpt) REVERT: E 459 TYR cc_start: 0.7226 (t80) cc_final: 0.6967 (t80) REVERT: F 208 LYS cc_start: 0.4875 (mmmt) cc_final: 0.3988 (mttm) REVERT: F 271 ILE cc_start: 0.7416 (pp) cc_final: 0.7213 (pp) REVERT: F 283 GLN cc_start: 0.6233 (OUTLIER) cc_final: 0.5582 (tt0) REVERT: F 377 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7210 (mm) REVERT: G 283 GLN cc_start: 0.6254 (OUTLIER) cc_final: 0.5607 (tt0) REVERT: G 491 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6297 (tt0) REVERT: H 271 ILE cc_start: 0.7445 (pp) cc_final: 0.7165 (pp) REVERT: H 283 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5519 (tt0) REVERT: H 450 LYS cc_start: 0.7692 (ttmm) cc_final: 0.7363 (ttpt) REVERT: H 459 TYR cc_start: 0.7097 (t80) cc_final: 0.6798 (t80) REVERT: H 491 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6028 (tt0) outliers start: 112 outliers final: 86 residues processed: 525 average time/residue: 0.3389 time to fit residues: 296.5743 Evaluate side-chains 513 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 414 time to evaluate : 2.739 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 491 GLU 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 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 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 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR 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 282 TYR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 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 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 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain 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 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 395 GLU Chi-restraints excluded: chain H residue 453 ILE 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: 0.0870 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 229 optimal weight: 0.7980 chunk 341 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.189121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.161719 restraints weight = 33406.168| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.96 r_work: 0.4136 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3742 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= 0.124 Angle : 0.587 7.609 39176 Z= 0.290 Chirality : 0.043 0.170 4600 Planarity : 0.004 0.054 4800 Dihedral : 16.878 178.062 4800 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.69 % Allowed : 20.22 % 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: -0.33 (0.14), residues: 3528 helix: 0.83 (0.15), residues: 1384 sheet: -0.24 (0.27), residues: 264 loop : -1.02 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 296 PHE 0.013 0.001 PHE C 35 TYR 0.010 0.001 TYR D 459 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1110) hydrogen bonds : angle 5.10099 ( 3114) covalent geometry : bond 0.00292 (28800) covalent geometry : angle 0.58691 (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 536 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 428 time to evaluate : 3.061 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4797 (mmmt) cc_final: 0.3858 (mttm) REVERT: A 450 LYS cc_start: 0.7856 (ttmm) cc_final: 0.7379 (ttpt) REVERT: A 459 TYR cc_start: 0.7174 (t80) cc_final: 0.6830 (t80) REVERT: B 208 LYS cc_start: 0.4879 (mmmt) cc_final: 0.3952 (mttm) REVERT: B 271 ILE cc_start: 0.7518 (pp) cc_final: 0.7262 (pp) REVERT: B 283 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.5709 (mt0) REVERT: B 377 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7220 (mm) REVERT: B 456 PHE cc_start: 0.7954 (t80) cc_final: 0.7514 (t80) REVERT: C 283 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.5797 (tt0) REVERT: C 491 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6198 (tt0) REVERT: D 208 LYS cc_start: 0.4884 (mmmt) cc_final: 0.3813 (mttm) REVERT: D 271 ILE cc_start: 0.7526 (pp) cc_final: 0.7256 (pp) REVERT: D 283 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.5677 (tt0) REVERT: E 208 LYS cc_start: 0.4801 (mmmt) cc_final: 0.3875 (mttm) REVERT: E 450 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7348 (ttpt) REVERT: E 459 TYR cc_start: 0.7210 (t80) cc_final: 0.6916 (t80) REVERT: F 208 LYS cc_start: 0.4805 (mmmt) cc_final: 0.3880 (mttm) REVERT: F 271 ILE cc_start: 0.7497 (pp) cc_final: 0.7287 (pp) REVERT: F 283 GLN cc_start: 0.6288 (OUTLIER) cc_final: 0.5586 (tt0) REVERT: F 377 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7244 (mm) REVERT: G 283 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5761 (tt0) REVERT: G 491 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6339 (tt0) REVERT: H 271 ILE cc_start: 0.7531 (pp) cc_final: 0.7242 (pp) REVERT: H 283 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.5686 (tt0) REVERT: H 450 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7370 (ttpt) REVERT: H 459 TYR cc_start: 0.7068 (t80) cc_final: 0.6777 (t80) REVERT: H 491 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6205 (tt0) outliers start: 108 outliers final: 92 residues processed: 513 average time/residue: 0.3513 time to fit residues: 298.9966 Evaluate side-chains 515 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 412 time to evaluate : 2.946 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 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 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 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR 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 282 TYR 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 370 VAL Chi-restraints excluded: chain E residue 383 THR 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 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 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain 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 283 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 290 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 318 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 chunk 184 optimal weight: 0.0050 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.4555 r_free = 0.4555 target = 0.189485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.162024 restraints weight = 33352.156| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.96 r_work: 0.4150 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3940 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= 0.122 Angle : 0.578 7.635 39176 Z= 0.288 Chirality : 0.043 0.142 4600 Planarity : 0.004 0.059 4800 Dihedral : 16.398 179.815 4800 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.62 % Allowed : 20.80 % Favored : 75.58 % 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: -0.31 (0.14), residues: 3528 helix: 0.85 (0.14), residues: 1392 sheet: -0.53 (0.31), residues: 224 loop : -0.96 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 125 PHE 0.012 0.001 PHE C 35 TYR 0.015 0.001 TYR E 258 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 1110) hydrogen bonds : angle 5.08365 ( 3114) covalent geometry : bond 0.00288 (28800) covalent geometry : angle 0.57822 (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 531 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 425 time to evaluate : 2.904 Fit side-chains REVERT: A 208 LYS cc_start: 0.4789 (mmmt) cc_final: 0.3829 (mttm) REVERT: A 450 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7298 (ttpt) REVERT: A 459 TYR cc_start: 0.7097 (t80) cc_final: 0.6741 (t80) REVERT: A 491 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6274 (tt0) REVERT: B 208 LYS cc_start: 0.4882 (mmmt) cc_final: 0.3912 (mttm) REVERT: B 271 ILE cc_start: 0.7532 (pp) cc_final: 0.7281 (pp) REVERT: B 283 GLN cc_start: 0.6271 (OUTLIER) cc_final: 0.5791 (mt0) REVERT: B 377 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7222 (mm) REVERT: B 491 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6223 (tt0) REVERT: C 283 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5778 (tt0) REVERT: C 491 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6277 (tt0) REVERT: D 208 LYS cc_start: 0.4972 (mmmt) cc_final: 0.3850 (mttm) REVERT: D 271 ILE cc_start: 0.7539 (pp) cc_final: 0.7270 (pp) REVERT: D 283 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.5637 (tt0) REVERT: E 208 LYS cc_start: 0.4790 (mmmt) cc_final: 0.3846 (mttm) REVERT: E 271 ILE cc_start: 0.7473 (pp) cc_final: 0.7232 (pp) REVERT: E 450 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7335 (ttpt) REVERT: E 459 TYR cc_start: 0.7162 (t80) cc_final: 0.6842 (t80) REVERT: F 208 LYS cc_start: 0.4798 (mmmt) cc_final: 0.3872 (mttm) REVERT: F 283 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.5754 (mt0) REVERT: F 377 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7252 (mm) REVERT: G 166 LEU cc_start: 0.6820 (mp) cc_final: 0.5992 (mt) REVERT: G 283 GLN cc_start: 0.6308 (OUTLIER) cc_final: 0.5645 (tt0) REVERT: G 491 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6248 (tt0) REVERT: H 166 LEU cc_start: 0.6793 (mp) cc_final: 0.6088 (mt) REVERT: H 271 ILE cc_start: 0.7539 (pp) cc_final: 0.7261 (pp) REVERT: H 283 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5667 (tt0) REVERT: H 450 LYS cc_start: 0.7733 (ttmm) cc_final: 0.7332 (ttpt) REVERT: H 459 TYR cc_start: 0.7088 (t80) cc_final: 0.6782 (t80) REVERT: H 491 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6286 (tt0) outliers start: 106 outliers final: 91 residues processed: 504 average time/residue: 0.3559 time to fit residues: 301.2222 Evaluate side-chains 517 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 413 time to evaluate : 2.811 ------------------------------------------------------------------------------- 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 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 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 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 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain 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 282 TYR 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 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain 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 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 208 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 chunk 328 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 163 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4550 r_free = 0.4550 target = 0.189051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.162002 restraints weight = 33400.166| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 1.91 r_work: 0.4158 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4026 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28800 Z= 0.124 Angle : 0.589 8.156 39176 Z= 0.291 Chirality : 0.043 0.143 4600 Planarity : 0.004 0.061 4800 Dihedral : 15.771 179.731 4800 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.55 % Allowed : 21.14 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.14), residues: 3528 helix: 0.87 (0.15), residues: 1392 sheet: -0.22 (0.27), residues: 264 loop : -1.02 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 93 PHE 0.013 0.001 PHE C 35 TYR 0.013 0.001 TYR E 289 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 1110) hydrogen bonds : angle 5.08353 ( 3114) covalent geometry : bond 0.00294 (28800) covalent geometry : angle 0.58900 (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 522 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 418 time to evaluate : 2.913 Fit side-chains REVERT: A 208 LYS cc_start: 0.4903 (mmmt) cc_final: 0.3838 (mttm) REVERT: A 450 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7273 (ttpt) REVERT: A 459 TYR cc_start: 0.7116 (t80) cc_final: 0.6786 (t80) REVERT: A 491 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: B 208 LYS cc_start: 0.4886 (mmmt) cc_final: 0.3908 (mttm) REVERT: B 271 ILE cc_start: 0.7516 (pp) cc_final: 0.7266 (pp) REVERT: B 283 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.5914 (mt0) REVERT: B 377 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7258 (mm) REVERT: B 491 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: C 283 GLN cc_start: 0.6425 (OUTLIER) cc_final: 0.6077 (tt0) REVERT: C 491 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6295 (tt0) REVERT: D 208 LYS cc_start: 0.4971 (mmmt) cc_final: 0.3866 (mttm) REVERT: D 254 GLU cc_start: 0.7507 (tp30) cc_final: 0.7210 (tp30) REVERT: D 271 ILE cc_start: 0.7570 (pp) cc_final: 0.7358 (pp) REVERT: D 283 GLN cc_start: 0.6284 (OUTLIER) cc_final: 0.5611 (tt0) REVERT: D 491 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6182 (tt0) REVERT: E 208 LYS cc_start: 0.4967 (mmmt) cc_final: 0.3861 (mttm) REVERT: E 450 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7299 (ttpt) REVERT: E 459 TYR cc_start: 0.7131 (t80) cc_final: 0.6768 (t80) REVERT: F 208 LYS cc_start: 0.4915 (mmmt) cc_final: 0.3871 (mttm) REVERT: F 283 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5749 (mt0) REVERT: F 377 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7268 (mm) REVERT: G 166 LEU cc_start: 0.6734 (mp) cc_final: 0.6019 (mt) REVERT: G 283 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5769 (tt0) REVERT: H 166 LEU cc_start: 0.6693 (mp) cc_final: 0.5995 (mt) REVERT: H 271 ILE cc_start: 0.7541 (pp) cc_final: 0.7269 (pp) REVERT: H 283 GLN cc_start: 0.6308 (OUTLIER) cc_final: 0.5650 (tt0) REVERT: H 450 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7333 (ttpt) REVERT: H 459 TYR cc_start: 0.7146 (t80) cc_final: 0.6847 (t80) outliers start: 104 outliers final: 91 residues processed: 496 average time/residue: 0.3788 time to fit residues: 319.3889 Evaluate side-chains 513 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 410 time to evaluate : 3.115 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 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 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 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain 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 282 TYR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU 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 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 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 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 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 109 optimal weight: 2.9990 chunk 308 optimal weight: 0.0870 chunk 192 optimal weight: 0.8980 chunk 345 optimal weight: 1.9990 chunk 274 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.189587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.163389 restraints weight = 33197.667| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 1.84 r_work: 0.4165 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4273 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= 0.128 Angle : 0.592 7.730 39176 Z= 0.292 Chirality : 0.043 0.146 4600 Planarity : 0.005 0.066 4800 Dihedral : 15.587 179.953 4800 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.65 % Allowed : 21.07 % Favored : 75.27 % 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: -0.29 (0.14), residues: 3528 helix: 0.88 (0.15), residues: 1392 sheet: -0.52 (0.31), residues: 224 loop : -0.96 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 93 PHE 0.013 0.001 PHE C 35 TYR 0.016 0.001 TYR E 289 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 1110) hydrogen bonds : angle 5.08660 ( 3114) covalent geometry : bond 0.00304 (28800) covalent geometry : angle 0.59182 (39176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17074.24 seconds wall clock time: 294 minutes 20.24 seconds (17660.24 seconds total)