Starting phenix.real_space_refine on Fri Jun 5 20:10:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9muc_48628/06_2026/9muc_48628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9muc_48628/06_2026/9muc_48628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9muc_48628/06_2026/9muc_48628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9muc_48628/06_2026/9muc_48628.map" model { file = "/net/cci-nas-00/data/ceres_data/9muc_48628/06_2026/9muc_48628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9muc_48628/06_2026/9muc_48628.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.277 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 24 5.49 5 S 144 5.16 5 C 14440 2.51 5 N 3912 2.21 5 O 4464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22984 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "C" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "D" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "E" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "F" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "G" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "H" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 6.31, per 1000 atoms: 0.27 Number of scatterers: 22984 At special positions: 0 Unit cell: (117.705, 116.82, 119.475, 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 144 16.00 P 24 15.00 O 4464 8.00 N 3912 7.00 C 14440 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 951.7 milliseconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 41.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 19 through 24 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 45 through 49 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.509A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.663A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 356 removed outlier: 4.061A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 24 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 45 through 49 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.711A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 356 removed outlier: 4.049A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 19 through 24 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 45 through 49 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.586A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.678A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 356 removed outlier: 4.071A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 19 through 24 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 45 through 49 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.714A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 356 removed outlier: 3.506A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 19 through 24 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 45 through 49 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 255 through 266 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.666A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 356 removed outlier: 4.053A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 19 through 24 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 45 through 49 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.682A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 356 removed outlier: 3.519A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 19 through 24 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 45 through 49 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.526A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.709A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.514A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 19 through 24 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 45 through 49 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.527A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.679A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 356 removed outlier: 4.077A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.122A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY A 302 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.599A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.594A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (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: 6.592A 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: 6.717A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY B 302 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU B 273 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL B 304 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.589A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.618A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.717A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLY C 302 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU C 273 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL C 304 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.608A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.635A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.723A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N GLY D 302 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.706A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLY E 302 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.604A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.606A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.703A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N GLY F 302 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.634A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.615A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.716A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N GLY G 302 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.595A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.090A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY H 302 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) 915 hydrogen bonds defined for protein. 2583 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: 4.64 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6690 1.34 - 1.46: 4219 1.46 - 1.59: 12187 1.59 - 1.72: 40 1.72 - 1.84: 240 Bond restraints: 23376 Sorted by residual: bond pdb=" C4A NAD D 602 " pdb=" C5A NAD D 602 " ideal model delta sigma weight residual 1.386 1.472 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C4A NAD C 602 " pdb=" C5A NAD C 602 " ideal model delta sigma weight residual 1.386 1.472 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C4A NAD E 602 " pdb=" C5A NAD E 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C4A NAD F 602 " pdb=" C5A NAD F 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C4A NAD H 602 " pdb=" C5A NAD H 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 23371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 25283 2.22 - 4.44: 5697 4.44 - 6.65: 592 6.65 - 8.87: 45 8.87 - 11.09: 23 Bond angle restraints: 31640 Sorted by residual: angle pdb=" N THR C 74 " pdb=" CA THR C 74 " pdb=" C THR C 74 " ideal model delta sigma weight residual 108.02 119.11 -11.09 1.75e+00 3.27e-01 4.02e+01 angle pdb=" N THR G 74 " pdb=" CA THR G 74 " pdb=" C THR G 74 " ideal model delta sigma weight residual 108.02 118.81 -10.79 1.75e+00 3.27e-01 3.80e+01 angle pdb=" N THR H 74 " pdb=" CA THR H 74 " pdb=" C THR H 74 " ideal model delta sigma weight residual 108.02 118.75 -10.73 1.75e+00 3.27e-01 3.76e+01 angle pdb=" N THR B 74 " pdb=" CA THR B 74 " pdb=" C THR B 74 " ideal model delta sigma weight residual 108.02 118.73 -10.71 1.75e+00 3.27e-01 3.75e+01 angle pdb=" N THR F 74 " pdb=" CA THR F 74 " pdb=" C THR F 74 " ideal model delta sigma weight residual 108.02 118.61 -10.59 1.75e+00 3.27e-01 3.66e+01 ... (remaining 31635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13117 17.90 - 35.81: 834 35.81 - 53.71: 294 53.71 - 71.61: 71 71.61 - 89.51: 12 Dihedral angle restraints: 14328 sinusoidal: 5856 harmonic: 8472 Sorted by residual: dihedral pdb=" C ALA E 392 " pdb=" N ALA E 392 " pdb=" CA ALA E 392 " pdb=" CB ALA E 392 " ideal model delta harmonic sigma weight residual -122.60 -132.86 10.26 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C ALA G 392 " pdb=" N ALA G 392 " pdb=" CA ALA G 392 " pdb=" CB ALA G 392 " ideal model delta harmonic sigma weight residual -122.60 -132.78 10.18 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" C ALA B 392 " pdb=" N ALA B 392 " pdb=" CA ALA B 392 " pdb=" CB ALA B 392 " ideal model delta harmonic sigma weight residual -122.60 -132.76 10.16 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 14325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2077 0.070 - 0.140: 1127 0.140 - 0.211: 327 0.211 - 0.281: 97 0.281 - 0.351: 20 Chirality restraints: 3648 Sorted by residual: chirality pdb=" CA ALA E 392 " pdb=" N ALA E 392 " pdb=" C ALA E 392 " pdb=" CB ALA E 392 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA ALA G 392 " pdb=" N ALA G 392 " pdb=" C ALA G 392 " pdb=" CB ALA G 392 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA ALA B 392 " pdb=" N ALA B 392 " pdb=" C ALA B 392 " pdb=" CB ALA B 392 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 3645 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IMP H 601 " 0.141 2.00e-02 2.50e+03 6.19e-02 1.05e+02 pdb=" C2 IMP H 601 " -0.024 2.00e-02 2.50e+03 pdb=" C4 IMP H 601 " -0.071 2.00e-02 2.50e+03 pdb=" C5 IMP H 601 " -0.040 2.00e-02 2.50e+03 pdb=" C6 IMP H 601 " 0.032 2.00e-02 2.50e+03 pdb=" C8 IMP H 601 " -0.014 2.00e-02 2.50e+03 pdb=" N1 IMP H 601 " 0.035 2.00e-02 2.50e+03 pdb=" N3 IMP H 601 " -0.052 2.00e-02 2.50e+03 pdb=" N7 IMP H 601 " -0.056 2.00e-02 2.50e+03 pdb=" N9 IMP H 601 " -0.028 2.00e-02 2.50e+03 pdb=" O6 IMP H 601 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 4 " -0.136 2.00e-02 2.50e+03 7.23e-02 1.05e+02 pdb=" CG TYR B 4 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 4 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR B 4 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR B 4 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR B 4 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR B 4 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 4 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP G 601 " 0.139 2.00e-02 2.50e+03 6.09e-02 1.02e+02 pdb=" C2 IMP G 601 " -0.023 2.00e-02 2.50e+03 pdb=" C4 IMP G 601 " -0.071 2.00e-02 2.50e+03 pdb=" C5 IMP G 601 " -0.039 2.00e-02 2.50e+03 pdb=" C6 IMP G 601 " 0.032 2.00e-02 2.50e+03 pdb=" C8 IMP G 601 " -0.009 2.00e-02 2.50e+03 pdb=" N1 IMP G 601 " 0.036 2.00e-02 2.50e+03 pdb=" N3 IMP G 601 " -0.050 2.00e-02 2.50e+03 pdb=" N7 IMP G 601 " -0.055 2.00e-02 2.50e+03 pdb=" N9 IMP G 601 " -0.031 2.00e-02 2.50e+03 pdb=" O6 IMP G 601 " 0.073 2.00e-02 2.50e+03 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 8544 2.92 - 3.42: 22307 3.42 - 3.91: 39821 3.91 - 4.41: 45945 4.41 - 4.90: 74907 Nonbonded interactions: 191524 Sorted by model distance: nonbonded pdb=" NE2 GLN C 469 " pdb=" O2B NAD D 602 " model vdw 2.427 3.120 nonbonded pdb=" NE2 GLN D 469 " pdb=" O2B NAD A 602 " model vdw 2.431 3.120 nonbonded pdb=" NE2 GLN E 469 " pdb=" O2B NAD F 602 " model vdw 2.435 3.120 nonbonded pdb=" NE2 GLN G 469 " pdb=" O2B NAD H 602 " model vdw 2.436 3.120 nonbonded pdb=" OG SER G 276 " pdb=" O1N NAD G 602 " model vdw 2.442 3.040 ... (remaining 191519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.990 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.016 0.529 23384 Z= 1.162 Angle : 1.828 11.090 31640 Z= 1.175 Chirality : 0.093 0.351 3648 Planarity : 0.013 0.096 3976 Dihedral : 13.713 89.511 8952 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.57 % Allowed : 3.87 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 2952 helix: 1.29 (0.15), residues: 1120 sheet: -0.43 (0.29), residues: 320 loop : 0.06 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG B 512 TYR 0.136 0.022 TYR B 4 PHE 0.059 0.014 PHE D 24 HIS 0.012 0.003 HIS C 504 Details of bonding type rmsd/Z covalent geometry : bond 0.01297 / 0.77 (23376) covalent geometry : angle 1.82789 / 1.17 (31640) hydrogen bonds : bond 0.18847 / 12.75 ( 915) hydrogen bonds : angle 6.21233 / 4.42 ( 2583) Misc. bond : bond 0.46945 / 22.69 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 419 time to evaluate : 1.010 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 1 MET cc_start: 0.5776 (mmp) cc_final: 0.5481 (mmp) REVERT: A 256 ASP cc_start: 0.7701 (m-30) cc_final: 0.7359 (m-30) REVERT: A 395 GLU cc_start: 0.7524 (mp0) cc_final: 0.7321 (mp0) REVERT: A 448 GLN cc_start: 0.7820 (pt0) cc_final: 0.7590 (pt0) REVERT: A 483 MET cc_start: 0.8610 (tmm) cc_final: 0.8158 (tmm) REVERT: B 1 MET cc_start: 0.5809 (mmp) cc_final: 0.5497 (mmp) REVERT: B 256 ASP cc_start: 0.7723 (m-30) cc_final: 0.7405 (m-30) REVERT: B 483 MET cc_start: 0.8540 (tmm) cc_final: 0.8018 (tmm) REVERT: B 498 GLN cc_start: 0.7239 (mt0) cc_final: 0.6903 (mt0) REVERT: C 1 MET cc_start: 0.5866 (mmp) cc_final: 0.5529 (mmp) REVERT: C 256 ASP cc_start: 0.7676 (m-30) cc_final: 0.7130 (m-30) REVERT: C 286 MET cc_start: 0.8897 (tpp) cc_final: 0.8668 (tpp) REVERT: C 483 MET cc_start: 0.8629 (tmm) cc_final: 0.8117 (tmm) REVERT: C 498 GLN cc_start: 0.7207 (mt0) cc_final: 0.6860 (mt0) REVERT: D 1 MET cc_start: 0.5863 (mmp) cc_final: 0.5551 (mmp) REVERT: D 243 GLN cc_start: 0.8071 (mt0) cc_final: 0.7865 (mt0) REVERT: D 255 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.6992 (p0) REVERT: D 256 ASP cc_start: 0.7595 (m-30) cc_final: 0.7211 (m-30) REVERT: D 448 GLN cc_start: 0.7680 (pt0) cc_final: 0.7424 (pt0) REVERT: D 483 MET cc_start: 0.8593 (tmm) cc_final: 0.8122 (tmm) REVERT: E 1 MET cc_start: 0.5793 (mmp) cc_final: 0.5483 (mmp) REVERT: E 255 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.6875 (p0) REVERT: E 256 ASP cc_start: 0.7707 (m-30) cc_final: 0.7278 (m-30) REVERT: E 395 GLU cc_start: 0.7540 (mp0) cc_final: 0.7325 (mp0) REVERT: E 483 MET cc_start: 0.8588 (tmm) cc_final: 0.8147 (tmm) REVERT: F 1 MET cc_start: 0.5916 (mmp) cc_final: 0.5511 (tpp) REVERT: F 255 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.6901 (p0) REVERT: F 256 ASP cc_start: 0.7677 (m-30) cc_final: 0.7301 (m-30) REVERT: F 483 MET cc_start: 0.8610 (tmm) cc_final: 0.8182 (tmm) REVERT: F 498 GLN cc_start: 0.7138 (mt0) cc_final: 0.6829 (mt0) REVERT: G 1 MET cc_start: 0.5831 (mmp) cc_final: 0.5583 (mmp) REVERT: G 256 ASP cc_start: 0.7648 (m-30) cc_final: 0.7340 (m-30) REVERT: G 448 GLN cc_start: 0.7545 (pt0) cc_final: 0.7296 (pt0) REVERT: G 483 MET cc_start: 0.8601 (tmm) cc_final: 0.8154 (tmm) REVERT: G 498 GLN cc_start: 0.7237 (mt0) cc_final: 0.6902 (mt0) REVERT: H 1 MET cc_start: 0.5848 (mmp) cc_final: 0.5562 (mmp) REVERT: H 256 ASP cc_start: 0.7710 (m-30) cc_final: 0.7379 (m-30) REVERT: H 395 GLU cc_start: 0.7545 (mp0) cc_final: 0.7324 (mp0) REVERT: H 483 MET cc_start: 0.8597 (tmm) cc_final: 0.8218 (tmm) REVERT: H 498 GLN cc_start: 0.7246 (mt0) cc_final: 0.6912 (mt0) outliers start: 61 outliers final: 27 residues processed: 470 average time/residue: 0.6170 time to fit residues: 332.6722 Evaluate side-chains 380 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 350 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 331 CYS Chi-restraints excluded: chain H residue 345 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN B 265 GLN C 21 GLN C 243 GLN C 265 GLN D 21 GLN E 21 GLN E 243 GLN F 21 GLN F 243 GLN G 21 GLN G 243 GLN H 21 GLN H 243 GLN H 265 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.199299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176986 restraints weight = 21911.131| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.25 r_work: 0.3955 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23384 Z= 0.139 Angle : 0.581 4.749 31640 Z= 0.319 Chirality : 0.043 0.127 3648 Planarity : 0.004 0.039 3976 Dihedral : 10.043 55.337 3880 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.90 % Allowed : 8.84 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2952 helix: 1.53 (0.16), residues: 1144 sheet: -0.67 (0.25), residues: 432 loop : 0.01 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 322 TYR 0.014 0.002 TYR G 12 PHE 0.013 0.002 PHE A 401 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (23376) covalent geometry : angle 0.58149 / 0.32 (31640) hydrogen bonds : bond 0.04948 / 3.32 ( 915) hydrogen bonds : angle 4.84509 / 3.44 ( 2583) Misc. bond : bond 0.00011 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 404 time to evaluate : 1.004 Fit side-chains REVERT: A 256 ASP cc_start: 0.7860 (m-30) cc_final: 0.7427 (m-30) REVERT: A 335 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6515 (mp0) REVERT: A 483 MET cc_start: 0.8602 (tmm) cc_final: 0.8168 (tmm) REVERT: B 75 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: B 256 ASP cc_start: 0.7739 (m-30) cc_final: 0.7211 (m-30) REVERT: B 277 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.5859 (tm-30) REVERT: B 335 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6651 (mp0) REVERT: B 420 MET cc_start: 0.7389 (ptm) cc_final: 0.7003 (ptt) REVERT: B 483 MET cc_start: 0.8601 (tmm) cc_final: 0.8084 (tmm) REVERT: C 1 MET cc_start: 0.5809 (mmp) cc_final: 0.5388 (mmp) REVERT: C 98 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: C 256 ASP cc_start: 0.7912 (m-30) cc_final: 0.7671 (m-30) REVERT: C 420 MET cc_start: 0.7271 (ptm) cc_final: 0.6837 (ptt) REVERT: C 483 MET cc_start: 0.8616 (tmm) cc_final: 0.8190 (tmm) REVERT: D 75 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: D 238 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.6110 (mttt) REVERT: D 256 ASP cc_start: 0.7622 (m-30) cc_final: 0.7214 (m-30) REVERT: D 277 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.6009 (tm-30) REVERT: D 448 GLN cc_start: 0.7581 (pt0) cc_final: 0.7372 (pt0) REVERT: D 483 MET cc_start: 0.8586 (tmm) cc_final: 0.8360 (tmm) REVERT: E 98 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: E 242 LYS cc_start: 0.7581 (mtmt) cc_final: 0.7371 (mptp) REVERT: E 255 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7243 (p0) REVERT: E 256 ASP cc_start: 0.7812 (m-30) cc_final: 0.7323 (m-30) REVERT: E 335 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6660 (mp0) REVERT: E 483 MET cc_start: 0.8592 (tmm) cc_final: 0.8066 (tmm) REVERT: F 1 MET cc_start: 0.5879 (mmp) cc_final: 0.5360 (mmp) REVERT: F 98 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: F 255 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7237 (p0) REVERT: F 256 ASP cc_start: 0.7743 (m-30) cc_final: 0.7223 (m-30) REVERT: F 335 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6592 (mp0) REVERT: F 420 MET cc_start: 0.7400 (ptm) cc_final: 0.6974 (ptt) REVERT: F 483 MET cc_start: 0.8621 (tmm) cc_final: 0.8218 (tmm) REVERT: G 1 MET cc_start: 0.5865 (mmp) cc_final: 0.5451 (mmp) REVERT: G 75 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: G 98 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: G 238 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6281 (mttt) REVERT: G 256 ASP cc_start: 0.7750 (m-30) cc_final: 0.7423 (m-30) REVERT: G 277 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.5778 (tm-30) REVERT: G 335 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6651 (mp0) REVERT: G 448 GLN cc_start: 0.7367 (pt0) cc_final: 0.7141 (pt0) REVERT: G 498 GLN cc_start: 0.7307 (mt0) cc_final: 0.7106 (mt0) REVERT: H 1 MET cc_start: 0.5955 (mmp) cc_final: 0.5660 (mmp) REVERT: H 75 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: H 98 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: H 256 ASP cc_start: 0.7818 (m-30) cc_final: 0.7441 (m-30) REVERT: H 335 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6537 (mp0) REVERT: H 420 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7146 (ptt) REVERT: H 483 MET cc_start: 0.8617 (tmm) cc_final: 0.8396 (tmm) outliers start: 69 outliers final: 22 residues processed: 446 average time/residue: 0.6567 time to fit residues: 334.0259 Evaluate side-chains 407 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 368 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 420 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 290 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN B 265 GLN C 243 GLN C 265 GLN E 265 GLN F 265 GLN G 243 GLN H 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.194450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.172092 restraints weight = 21898.408| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.25 r_work: 0.3900 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 23384 Z= 0.260 Angle : 0.760 6.250 31640 Z= 0.413 Chirality : 0.051 0.172 3648 Planarity : 0.005 0.041 3976 Dihedral : 10.347 54.837 3868 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.08 % Allowed : 8.88 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 2952 helix: 0.94 (0.15), residues: 1144 sheet: -0.68 (0.27), residues: 368 loop : -0.31 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 322 TYR 0.020 0.003 TYR B 348 PHE 0.016 0.003 PHE A 401 HIS 0.004 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.26 (23376) covalent geometry : angle 0.76008 / 0.41 (31640) hydrogen bonds : bond 0.06627 / 4.44 ( 915) hydrogen bonds : angle 5.16413 / 3.67 ( 2583) Misc. bond : bond 0.00105 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 364 time to evaluate : 1.013 Fit side-chains REVERT: A 98 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: A 256 ASP cc_start: 0.7779 (m-30) cc_final: 0.7334 (m-30) REVERT: A 277 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.6669 (tp40) REVERT: A 483 MET cc_start: 0.8546 (tmm) cc_final: 0.8010 (tmm) REVERT: B 98 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: B 242 LYS cc_start: 0.7601 (mtpm) cc_final: 0.7320 (mptp) REVERT: B 256 ASP cc_start: 0.7685 (m-30) cc_final: 0.7223 (m-30) REVERT: B 483 MET cc_start: 0.8551 (tmm) cc_final: 0.7958 (tmm) REVERT: C 1 MET cc_start: 0.5946 (mmp) cc_final: 0.5507 (mmp) REVERT: C 98 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: C 242 LYS cc_start: 0.7610 (mtpm) cc_final: 0.7409 (mptp) REVERT: C 256 ASP cc_start: 0.7787 (m-30) cc_final: 0.7503 (m-30) REVERT: C 277 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.6813 (tp40) REVERT: C 455 LYS cc_start: 0.7590 (pttt) cc_final: 0.7335 (ttpp) REVERT: C 483 MET cc_start: 0.8565 (tmm) cc_final: 0.8041 (tmm) REVERT: D 98 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: D 255 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7381 (p0) REVERT: D 256 ASP cc_start: 0.7674 (m-30) cc_final: 0.7238 (m-30) REVERT: D 448 GLN cc_start: 0.7631 (pt0) cc_final: 0.7381 (pt0) REVERT: D 483 MET cc_start: 0.8546 (tmm) cc_final: 0.7950 (tmm) REVERT: E 98 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: E 255 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7265 (p0) REVERT: E 256 ASP cc_start: 0.7761 (m-30) cc_final: 0.7288 (m-30) REVERT: E 277 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.6691 (tp40) REVERT: E 483 MET cc_start: 0.8541 (tmm) cc_final: 0.7952 (tmm) REVERT: F 1 MET cc_start: 0.6154 (mmp) cc_final: 0.5652 (mmp) REVERT: F 98 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: F 255 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7271 (p0) REVERT: F 256 ASP cc_start: 0.7704 (m-30) cc_final: 0.7219 (m-30) REVERT: F 277 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.6855 (tp40) REVERT: F 335 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6680 (mp0) REVERT: F 406 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5984 (pp) REVERT: F 483 MET cc_start: 0.8573 (tmm) cc_final: 0.8008 (tmm) REVERT: G 1 MET cc_start: 0.6002 (mmp) cc_final: 0.5562 (mmp) REVERT: G 98 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: G 256 ASP cc_start: 0.7825 (m-30) cc_final: 0.7444 (m-30) REVERT: G 277 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.6300 (tm-30) REVERT: G 335 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6835 (mm-30) REVERT: G 448 GLN cc_start: 0.7477 (pt0) cc_final: 0.7273 (pt0) REVERT: H 1 MET cc_start: 0.6074 (mmp) cc_final: 0.5746 (mmp) REVERT: H 98 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: H 256 ASP cc_start: 0.7779 (m-30) cc_final: 0.7322 (m-30) REVERT: H 277 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.6752 (tp40) REVERT: H 483 MET cc_start: 0.8572 (tmm) cc_final: 0.7996 (tmm) outliers start: 97 outliers final: 35 residues processed: 429 average time/residue: 0.6695 time to fit residues: 325.4942 Evaluate side-chains 402 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 349 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 420 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 37 optimal weight: 10.0000 chunk 217 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 259 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 GLN C 265 GLN D 265 GLN E 265 GLN F 243 GLN F 265 GLN G 243 GLN G 265 GLN H 21 GLN H 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.199415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177721 restraints weight = 22115.842| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.25 r_work: 0.3962 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 23384 Z= 0.115 Angle : 0.534 4.631 31640 Z= 0.295 Chirality : 0.042 0.129 3648 Planarity : 0.004 0.043 3976 Dihedral : 9.941 53.970 3868 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.96 % Allowed : 9.81 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 2952 helix: 1.51 (0.16), residues: 1144 sheet: -0.65 (0.26), residues: 416 loop : -0.22 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 105 TYR 0.015 0.002 TYR H 12 PHE 0.013 0.001 PHE A 401 HIS 0.003 0.000 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (23376) covalent geometry : angle 0.53448 / 0.29 (31640) hydrogen bonds : bond 0.04212 / 2.82 ( 915) hydrogen bonds : angle 4.59444 / 3.26 ( 2583) Misc. bond : bond 0.00013 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 378 time to evaluate : 0.896 Fit side-chains REVERT: A 75 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: A 98 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: A 256 ASP cc_start: 0.7835 (m-30) cc_final: 0.7339 (m-30) REVERT: A 420 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6879 (ptt) REVERT: A 483 MET cc_start: 0.8580 (tmm) cc_final: 0.7947 (tmm) REVERT: B 75 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: B 98 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: B 256 ASP cc_start: 0.7684 (m-30) cc_final: 0.7179 (m-30) REVERT: B 277 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.6072 (tm-30) REVERT: B 483 MET cc_start: 0.8576 (tmm) cc_final: 0.7945 (tmm) REVERT: C 1 MET cc_start: 0.6109 (mmp) cc_final: 0.5767 (mmp) REVERT: C 75 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: C 256 ASP cc_start: 0.7834 (m-30) cc_final: 0.7562 (m-30) REVERT: C 420 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7212 (ptt) REVERT: C 455 LYS cc_start: 0.7454 (pttt) cc_final: 0.7159 (ttpp) REVERT: C 483 MET cc_start: 0.8558 (tmm) cc_final: 0.7903 (tmm) REVERT: D 75 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: D 98 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: D 255 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7499 (p0) REVERT: D 256 ASP cc_start: 0.7671 (m-30) cc_final: 0.7253 (m-30) REVERT: D 277 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.6151 (tm-30) REVERT: D 483 MET cc_start: 0.8587 (tmm) cc_final: 0.7957 (tmm) REVERT: E 98 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: E 242 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7525 (mttp) REVERT: E 255 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7431 (p0) REVERT: E 256 ASP cc_start: 0.7747 (m-30) cc_final: 0.7241 (m-30) REVERT: E 483 MET cc_start: 0.8564 (tmm) cc_final: 0.7914 (tmm) REVERT: F 1 MET cc_start: 0.6038 (mmp) cc_final: 0.5521 (mmp) REVERT: F 98 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: F 255 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7379 (p0) REVERT: F 256 ASP cc_start: 0.7724 (m-30) cc_final: 0.7228 (m-30) REVERT: F 420 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7174 (ptt) REVERT: F 483 MET cc_start: 0.8579 (tmm) cc_final: 0.7955 (tmm) REVERT: G 1 MET cc_start: 0.6063 (mmp) cc_final: 0.5743 (mmp) REVERT: G 75 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: G 242 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7473 (mptp) REVERT: G 256 ASP cc_start: 0.7839 (m-30) cc_final: 0.7356 (m-30) REVERT: G 277 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.6126 (tm-30) REVERT: G 483 MET cc_start: 0.8443 (tmm) cc_final: 0.8014 (tmm) REVERT: H 1 MET cc_start: 0.6053 (mmp) cc_final: 0.5737 (mmp) REVERT: H 98 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: H 256 ASP cc_start: 0.7798 (m-30) cc_final: 0.7380 (m-30) REVERT: H 335 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6510 (mp0) REVERT: H 420 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6967 (ptt) REVERT: H 483 MET cc_start: 0.8592 (tmm) cc_final: 0.7968 (tmm) outliers start: 94 outliers final: 36 residues processed: 447 average time/residue: 0.6280 time to fit residues: 321.1748 Evaluate side-chains 425 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 367 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 420 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 226 optimal weight: 0.5980 chunk 183 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN C 243 GLN D 265 GLN E 265 GLN F 265 GLN G 243 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.201057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.179478 restraints weight = 21984.545| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.24 r_work: 0.3983 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23384 Z= 0.103 Angle : 0.503 4.558 31640 Z= 0.277 Chirality : 0.041 0.128 3648 Planarity : 0.004 0.043 3976 Dihedral : 9.770 56.819 3868 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.84 % Allowed : 9.68 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 2952 helix: 1.67 (0.16), residues: 1144 sheet: -0.62 (0.26), residues: 416 loop : -0.07 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 105 TYR 0.013 0.001 TYR B 348 PHE 0.012 0.001 PHE H 401 HIS 0.003 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (23376) covalent geometry : angle 0.50292 / 0.28 (31640) hydrogen bonds : bond 0.03823 / 2.56 ( 915) hydrogen bonds : angle 4.39187 / 3.12 ( 2583) Misc. bond : bond 0.00015 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 390 time to evaluate : 0.889 Fit side-chains REVERT: A 75 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: A 98 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 256 ASP cc_start: 0.7803 (m-30) cc_final: 0.7378 (m-30) REVERT: A 277 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.5548 (tm-30) REVERT: A 483 MET cc_start: 0.8568 (tmm) cc_final: 0.7940 (tmm) REVERT: A 491 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 75 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: B 256 ASP cc_start: 0.7663 (m-30) cc_final: 0.7149 (m-30) REVERT: B 277 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.5710 (tm-30) REVERT: B 491 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: C 1 MET cc_start: 0.6070 (mmp) cc_final: 0.5718 (mmp) REVERT: C 75 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: C 256 ASP cc_start: 0.7792 (m-30) cc_final: 0.7565 (m-30) REVERT: C 277 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.5513 (tm-30) REVERT: C 386 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7738 (ptt) REVERT: C 483 MET cc_start: 0.8539 (tmm) cc_final: 0.7882 (tmm) REVERT: C 491 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: D 75 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: D 255 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7423 (p0) REVERT: D 256 ASP cc_start: 0.7656 (m-30) cc_final: 0.7259 (m-30) REVERT: D 277 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.5798 (tm-30) REVERT: D 483 MET cc_start: 0.8575 (tmm) cc_final: 0.7943 (tmm) REVERT: D 491 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: E 75 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: E 98 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: E 255 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7424 (p0) REVERT: E 256 ASP cc_start: 0.7741 (m-30) cc_final: 0.7231 (m-30) REVERT: E 277 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.5548 (tm-30) REVERT: E 491 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: F 1 MET cc_start: 0.5967 (mmp) cc_final: 0.5444 (mmp) REVERT: F 98 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: F 255 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7477 (p0) REVERT: F 256 ASP cc_start: 0.7707 (m-30) cc_final: 0.7189 (m-30) REVERT: F 277 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.5497 (tm-30) REVERT: F 491 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: G 75 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: G 242 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7496 (mptp) REVERT: G 256 ASP cc_start: 0.7785 (m-30) cc_final: 0.7488 (m-30) REVERT: G 277 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.5773 (tm-30) REVERT: G 483 MET cc_start: 0.8437 (tmm) cc_final: 0.7946 (tmm) REVERT: G 491 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: H 75 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: H 98 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: H 256 ASP cc_start: 0.7735 (m-30) cc_final: 0.7376 (m-30) REVERT: H 277 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.5492 (tm-30) REVERT: H 335 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6564 (mp0) REVERT: H 420 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7052 (ptt) REVERT: H 483 MET cc_start: 0.8589 (tmm) cc_final: 0.7971 (tmm) REVERT: H 491 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7762 (tt0) outliers start: 115 outliers final: 33 residues processed: 470 average time/residue: 0.6086 time to fit residues: 328.9576 Evaluate side-chains 431 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 366 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 66 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN C 243 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 21 GLN F 265 GLN G 21 GLN G 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.194445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.172470 restraints weight = 21788.489| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.23 r_work: 0.3899 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 23384 Z= 0.294 Angle : 0.783 6.159 31640 Z= 0.426 Chirality : 0.054 0.208 3648 Planarity : 0.005 0.045 3976 Dihedral : 10.478 58.744 3868 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.87 % Allowed : 11.03 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 2952 helix: 0.89 (0.15), residues: 1144 sheet: -0.72 (0.28), residues: 368 loop : -0.33 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG G 322 TYR 0.021 0.003 TYR B 348 PHE 0.018 0.003 PHE A 401 HIS 0.004 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 (23376) covalent geometry : angle 0.78282 / 0.43 (31640) hydrogen bonds : bond 0.06692 / 4.48 ( 915) hydrogen bonds : angle 5.09838 / 3.63 ( 2583) Misc. bond : bond 0.00095 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 370 time to evaluate : 0.968 Fit side-chains REVERT: A 98 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: A 256 ASP cc_start: 0.7797 (m-30) cc_final: 0.7363 (m-30) REVERT: A 277 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.6028 (tm-30) REVERT: A 335 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: B 98 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: B 256 ASP cc_start: 0.7702 (m-30) cc_final: 0.7240 (m-30) REVERT: B 277 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.6138 (tm-30) REVERT: C 1 MET cc_start: 0.6071 (mmp) cc_final: 0.5621 (mmp) REVERT: C 98 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: C 256 ASP cc_start: 0.7840 (m-30) cc_final: 0.7553 (m-30) REVERT: C 277 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.6256 (tm-30) REVERT: C 455 LYS cc_start: 0.7587 (pttt) cc_final: 0.7273 (ttpp) REVERT: D 98 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: D 255 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7385 (p0) REVERT: D 256 ASP cc_start: 0.7722 (m-30) cc_final: 0.7277 (m-30) REVERT: D 277 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.6150 (tm-30) REVERT: E 98 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: E 255 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7287 (p0) REVERT: E 256 ASP cc_start: 0.7742 (m-30) cc_final: 0.7281 (m-30) REVERT: E 277 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.6229 (tm-30) REVERT: F 1 MET cc_start: 0.6057 (mmp) cc_final: 0.5556 (mmp) REVERT: F 98 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: F 255 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7271 (p0) REVERT: F 256 ASP cc_start: 0.7688 (m-30) cc_final: 0.7262 (m-30) REVERT: F 277 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: F 335 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6574 (mp0) REVERT: G 98 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: G 256 ASP cc_start: 0.7832 (m-30) cc_final: 0.7425 (m-30) REVERT: G 277 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.6206 (tm-30) REVERT: H 98 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: H 256 ASP cc_start: 0.7834 (m-30) cc_final: 0.7421 (m-30) REVERT: H 277 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.5959 (tm-30) outliers start: 92 outliers final: 42 residues processed: 437 average time/residue: 0.6512 time to fit residues: 323.8443 Evaluate side-chains 416 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 354 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 406 ILE Chi-restraints excluded: chain H residue 420 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 41 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 279 optimal weight: 0.5980 chunk 252 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 48 GLN C 21 GLN C 243 GLN C 265 GLN D 21 GLN D 265 GLN E 48 GLN E 265 GLN F 21 GLN F 243 GLN F 265 GLN G 21 GLN G 48 GLN G 243 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.199892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.178264 restraints weight = 21910.458| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.23 r_work: 0.3967 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23384 Z= 0.110 Angle : 0.525 5.308 31640 Z= 0.289 Chirality : 0.042 0.128 3648 Planarity : 0.004 0.040 3976 Dihedral : 10.019 57.205 3868 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.37 % Allowed : 11.32 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2952 helix: 1.51 (0.16), residues: 1144 sheet: -0.75 (0.26), residues: 416 loop : -0.19 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 105 TYR 0.015 0.001 TYR H 12 PHE 0.013 0.001 PHE A 401 HIS 0.003 0.000 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (23376) covalent geometry : angle 0.52465 / 0.29 (31640) hydrogen bonds : bond 0.03986 / 2.67 ( 915) hydrogen bonds : angle 4.50565 / 3.20 ( 2583) Misc. bond : bond 0.00007 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 380 time to evaluate : 0.845 Fit side-chains REVERT: A 75 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: A 98 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: A 256 ASP cc_start: 0.7799 (m-30) cc_final: 0.7311 (m-30) REVERT: A 277 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.5547 (tm-30) REVERT: A 483 MET cc_start: 0.8535 (tmm) cc_final: 0.8151 (tmm) REVERT: B 75 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: B 98 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: B 256 ASP cc_start: 0.7689 (m-30) cc_final: 0.7213 (m-30) REVERT: B 277 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.5978 (tm-30) REVERT: B 483 MET cc_start: 0.8415 (tmm) cc_final: 0.7973 (tmm) REVERT: C 1 MET cc_start: 0.6069 (mmp) cc_final: 0.5636 (mmp) REVERT: C 75 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: C 98 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: C 256 ASP cc_start: 0.7797 (m-30) cc_final: 0.7529 (m-30) REVERT: C 277 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.5533 (tm-30) REVERT: C 420 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7197 (ptt) REVERT: C 455 LYS cc_start: 0.7480 (pttt) cc_final: 0.7154 (ttpp) REVERT: C 483 MET cc_start: 0.8414 (tmm) cc_final: 0.7923 (tmm) REVERT: D 75 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: D 98 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: D 255 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7475 (p0) REVERT: D 256 ASP cc_start: 0.7647 (m-30) cc_final: 0.7231 (m-30) REVERT: D 277 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.6148 (tm-30) REVERT: D 483 MET cc_start: 0.8564 (tmm) cc_final: 0.8194 (tmm) REVERT: E 75 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: E 98 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: E 255 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7371 (p0) REVERT: E 256 ASP cc_start: 0.7724 (m-30) cc_final: 0.7231 (m-30) REVERT: E 277 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.5562 (tm-30) REVERT: E 483 MET cc_start: 0.8401 (tmm) cc_final: 0.7968 (tmm) REVERT: F 1 MET cc_start: 0.5962 (mmp) cc_final: 0.5446 (mmp) REVERT: F 98 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: F 255 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7368 (p0) REVERT: F 256 ASP cc_start: 0.7679 (m-30) cc_final: 0.7210 (m-30) REVERT: F 277 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.5502 (tm-30) REVERT: F 335 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6561 (mp0) REVERT: F 483 MET cc_start: 0.8400 (tmm) cc_final: 0.7970 (tmm) REVERT: G 75 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: G 98 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7007 (mm-30) REVERT: G 242 LYS cc_start: 0.7723 (mtmt) cc_final: 0.7506 (mptp) REVERT: G 256 ASP cc_start: 0.7787 (m-30) cc_final: 0.7334 (m-30) REVERT: G 277 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: H 98 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: H 256 ASP cc_start: 0.7770 (m-30) cc_final: 0.7316 (m-30) REVERT: H 277 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.5493 (tm-30) REVERT: H 420 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7143 (ptt) REVERT: H 483 MET cc_start: 0.8564 (tmm) cc_final: 0.8194 (tmm) outliers start: 80 outliers final: 34 residues processed: 437 average time/residue: 0.6381 time to fit residues: 317.9746 Evaluate side-chains 424 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 363 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 406 ILE Chi-restraints excluded: chain H residue 420 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN B 265 GLN B 478 GLN C 21 GLN C 243 GLN D 265 GLN E 265 GLN F 265 GLN G 243 GLN H 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.199366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177700 restraints weight = 21879.625| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.23 r_work: 0.3961 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23384 Z= 0.119 Angle : 0.535 4.930 31640 Z= 0.293 Chirality : 0.042 0.131 3648 Planarity : 0.004 0.045 3976 Dihedral : 10.034 58.276 3868 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.00 % Allowed : 11.62 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2952 helix: 1.58 (0.16), residues: 1144 sheet: -0.76 (0.26), residues: 416 loop : -0.13 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 105 TYR 0.014 0.002 TYR A 348 PHE 0.014 0.001 PHE A 401 HIS 0.003 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (23376) covalent geometry : angle 0.53516 / 0.29 (31640) hydrogen bonds : bond 0.04246 / 2.84 ( 915) hydrogen bonds : angle 4.43314 / 3.15 ( 2583) Misc. bond : bond 0.00019 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 369 time to evaluate : 0.815 Fit side-chains REVERT: A 75 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: A 98 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: A 256 ASP cc_start: 0.7806 (m-30) cc_final: 0.7317 (m-30) REVERT: A 277 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.5567 (tm-30) REVERT: A 483 MET cc_start: 0.8588 (tmm) cc_final: 0.8051 (tmm) REVERT: A 491 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: B 75 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: B 256 ASP cc_start: 0.7697 (m-30) cc_final: 0.7211 (m-30) REVERT: B 277 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.6056 (tm-30) REVERT: B 491 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: C 1 MET cc_start: 0.6077 (mmp) cc_final: 0.5632 (mmp) REVERT: C 75 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: C 98 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: C 256 ASP cc_start: 0.7854 (m-30) cc_final: 0.7567 (m-30) REVERT: C 277 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.5564 (tm-30) REVERT: C 420 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6930 (ptt) REVERT: C 455 LYS cc_start: 0.7428 (pttt) cc_final: 0.7092 (ttpp) REVERT: C 483 MET cc_start: 0.8480 (tmm) cc_final: 0.7938 (tmm) REVERT: C 491 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: D 75 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: D 98 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: D 255 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7494 (p0) REVERT: D 256 ASP cc_start: 0.7653 (m-30) cc_final: 0.7197 (m-30) REVERT: D 277 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.6193 (tm-30) REVERT: D 483 MET cc_start: 0.8595 (tmm) cc_final: 0.8079 (tmm) REVERT: D 491 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: E 75 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: E 98 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: E 255 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7377 (p0) REVERT: E 256 ASP cc_start: 0.7732 (m-30) cc_final: 0.7236 (m-30) REVERT: E 277 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.5584 (tm-30) REVERT: E 483 MET cc_start: 0.8464 (tmm) cc_final: 0.7912 (tmm) REVERT: E 491 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: F 1 MET cc_start: 0.5941 (mmp) cc_final: 0.5423 (mmp) REVERT: F 98 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: F 255 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7398 (p0) REVERT: F 256 ASP cc_start: 0.7677 (m-30) cc_final: 0.7200 (m-30) REVERT: F 277 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.5514 (tm-30) REVERT: F 483 MET cc_start: 0.8468 (tmm) cc_final: 0.7921 (tmm) REVERT: F 491 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: G 75 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: G 256 ASP cc_start: 0.7802 (m-30) cc_final: 0.7375 (m-30) REVERT: G 277 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: G 491 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: H 98 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: H 256 ASP cc_start: 0.7763 (m-30) cc_final: 0.7329 (m-30) REVERT: H 277 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.5522 (tm-30) REVERT: H 420 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6887 (ptt) REVERT: H 483 MET cc_start: 0.8602 (tmm) cc_final: 0.8076 (tmm) REVERT: H 491 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7772 (tt0) outliers start: 95 outliers final: 36 residues processed: 430 average time/residue: 0.6392 time to fit residues: 313.7235 Evaluate side-chains 435 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 366 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 2 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 265 optimal weight: 0.6980 chunk 138 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN B 478 GLN C 265 GLN D 265 GLN E 21 GLN E 265 GLN G 48 GLN H 21 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.200971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.179419 restraints weight = 21968.322| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.23 r_work: 0.3982 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3897 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23384 Z= 0.104 Angle : 0.503 5.793 31640 Z= 0.275 Chirality : 0.041 0.127 3648 Planarity : 0.004 0.046 3976 Dihedral : 9.907 58.683 3868 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.70 % Allowed : 11.91 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2952 helix: 1.66 (0.16), residues: 1144 sheet: -0.85 (0.26), residues: 416 loop : -0.08 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 105 TYR 0.014 0.001 TYR C 348 PHE 0.013 0.001 PHE A 401 HIS 0.003 0.000 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (23376) covalent geometry : angle 0.50273 / 0.28 (31640) hydrogen bonds : bond 0.03778 / 2.53 ( 915) hydrogen bonds : angle 4.32014 / 3.07 ( 2583) Misc. bond : bond 0.00011 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 374 time to evaluate : 0.821 Fit side-chains REVERT: A 75 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: A 98 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: A 256 ASP cc_start: 0.7779 (m-30) cc_final: 0.7362 (m-30) REVERT: A 277 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.5551 (tm-30) REVERT: A 483 MET cc_start: 0.8572 (tmm) cc_final: 0.7865 (tmm) REVERT: A 491 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: B 75 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: B 256 ASP cc_start: 0.7682 (m-30) cc_final: 0.7192 (m-30) REVERT: B 277 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.5718 (tm-30) REVERT: B 491 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: C 75 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: C 256 ASP cc_start: 0.7836 (m-30) cc_final: 0.7569 (m-30) REVERT: C 277 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.5520 (tm-30) REVERT: C 455 LYS cc_start: 0.7408 (pttt) cc_final: 0.7068 (ttpp) REVERT: C 483 MET cc_start: 0.8450 (tmm) cc_final: 0.7840 (tmm) REVERT: C 491 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: D 75 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: D 256 ASP cc_start: 0.7645 (m-30) cc_final: 0.7203 (m-30) REVERT: D 277 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.6114 (tm-30) REVERT: D 483 MET cc_start: 0.8589 (tmm) cc_final: 0.7894 (tmm) REVERT: D 491 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: E 75 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: E 98 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: E 255 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7466 (p0) REVERT: E 256 ASP cc_start: 0.7706 (m-30) cc_final: 0.7193 (m-30) REVERT: E 277 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.5490 (tm-30) REVERT: E 491 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: F 1 MET cc_start: 0.5944 (mmp) cc_final: 0.5428 (mmp) REVERT: F 98 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7121 (mm-30) REVERT: F 255 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7459 (p0) REVERT: F 256 ASP cc_start: 0.7676 (m-30) cc_final: 0.7178 (m-30) REVERT: F 277 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.5455 (tm-30) REVERT: F 491 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: G 75 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: G 256 ASP cc_start: 0.7786 (m-30) cc_final: 0.7346 (m-30) REVERT: G 277 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.6016 (tm-30) REVERT: G 491 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: H 98 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: H 256 ASP cc_start: 0.7727 (m-30) cc_final: 0.7312 (m-30) REVERT: H 277 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.5503 (tm-30) REVERT: H 420 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7072 (ptt) REVERT: H 483 MET cc_start: 0.8597 (tmm) cc_final: 0.7908 (tmm) REVERT: H 491 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7765 (tt0) outliers start: 88 outliers final: 36 residues processed: 431 average time/residue: 0.6456 time to fit residues: 317.5834 Evaluate side-chains 430 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 365 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 74 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 185 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 21 GLN B 478 GLN C 265 GLN D 265 GLN E 265 GLN F 265 GLN G 48 GLN G 265 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.194974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.172923 restraints weight = 21743.587| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.24 r_work: 0.3909 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 23384 Z= 0.250 Angle : 0.725 6.093 31640 Z= 0.395 Chirality : 0.051 0.185 3648 Planarity : 0.005 0.047 3976 Dihedral : 10.507 59.967 3868 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.03 % Allowed : 13.05 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 2952 helix: 1.08 (0.15), residues: 1144 sheet: -0.89 (0.26), residues: 416 loop : -0.29 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 105 TYR 0.019 0.003 TYR C 348 PHE 0.016 0.003 PHE E 401 HIS 0.003 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.25 (23376) covalent geometry : angle 0.72527 / 0.39 (31640) hydrogen bonds : bond 0.06153 / 4.12 ( 915) hydrogen bonds : angle 4.92354 / 3.50 ( 2583) Misc. bond : bond 0.00068 / 0.03 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 368 time to evaluate : 0.935 Fit side-chains REVERT: A 98 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: A 256 ASP cc_start: 0.7804 (m-30) cc_final: 0.7445 (m-30) REVERT: A 277 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.6027 (tm-30) REVERT: B 75 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: B 256 ASP cc_start: 0.7661 (m-30) cc_final: 0.7213 (m-30) REVERT: B 277 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.6337 (tm-30) REVERT: C 75 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: C 256 ASP cc_start: 0.7897 (m-30) cc_final: 0.7562 (m-30) REVERT: C 277 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.6252 (tm-30) REVERT: C 455 LYS cc_start: 0.7514 (pttt) cc_final: 0.7213 (ttpp) REVERT: D 75 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: D 98 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: D 256 ASP cc_start: 0.7652 (m-30) cc_final: 0.7229 (m-30) REVERT: E 75 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: E 98 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7230 (mm-30) REVERT: E 255 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7316 (p0) REVERT: E 256 ASP cc_start: 0.7724 (m-30) cc_final: 0.7286 (m-30) REVERT: E 277 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.6253 (tm-30) REVERT: F 1 MET cc_start: 0.6101 (mmp) cc_final: 0.5629 (mmp) REVERT: F 98 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7269 (mm-30) REVERT: F 255 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7241 (p0) REVERT: F 256 ASP cc_start: 0.7651 (m-30) cc_final: 0.7218 (m-30) REVERT: F 277 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.6306 (tm-30) REVERT: G 256 ASP cc_start: 0.7827 (m-30) cc_final: 0.7425 (m-30) REVERT: G 277 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.6171 (tm-30) REVERT: H 98 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: H 256 ASP cc_start: 0.7755 (m-30) cc_final: 0.7326 (m-30) REVERT: H 277 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.6064 (tm-30) outliers start: 72 outliers final: 40 residues processed: 423 average time/residue: 0.6744 time to fit residues: 324.3827 Evaluate side-chains 419 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 361 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 466 HIS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 406 ILE Chi-restraints excluded: chain H residue 420 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 265 GLN B 21 GLN B 478 GLN C 21 GLN C 48 GLN C 265 GLN D 21 GLN D 48 GLN D 265 GLN E 21 GLN E 48 GLN E 265 GLN F 21 GLN F 48 GLN F 265 GLN G 21 GLN G 48 GLN G 265 GLN H 21 GLN H 48 GLN H 265 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.199916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.178464 restraints weight = 21784.221| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.23 r_work: 0.3974 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23384 Z= 0.104 Angle : 0.513 5.874 31640 Z= 0.280 Chirality : 0.041 0.127 3648 Planarity : 0.004 0.046 3976 Dihedral : 10.123 59.935 3868 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.78 % Allowed : 12.96 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2952 helix: 1.61 (0.16), residues: 1144 sheet: -0.94 (0.25), residues: 416 loop : -0.16 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 105 TYR 0.014 0.002 TYR B 12 PHE 0.013 0.001 PHE H 401 HIS 0.003 0.000 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (23376) covalent geometry : angle 0.51264 / 0.28 (31640) hydrogen bonds : bond 0.03728 / 2.49 ( 915) hydrogen bonds : angle 4.39355 / 3.12 ( 2583) Misc. bond : bond 0.00021 / 0.01 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10279.22 seconds wall clock time: 175 minutes 31.46 seconds (10531.46 seconds total)