Starting phenix.real_space_refine on Sun Sep 13 12:57:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9muc_48628/09_2026/9muc_48628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9muc_48628/09_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_48628/09_2026/9muc_48628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9muc_48628/09_2026/9muc_48628.map" model { file = "/net/cci-nas-00/data/ceres_data/9muc_48628/09_2026/9muc_48628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9muc_48628/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.48, per 1000 atoms: 0.24 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.70 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: 4.39 Time building geometry restraints manager: 2.63 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: 25279 2.22 - 4.44: 5711 4.44 - 6.65: 582 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: 2092 0.070 - 0.140: 1112 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.310 Find NCS groups from input model: 0.680 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: 0.010 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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= 1.161 Angle : 1.827 11.090 31640 Z= 1.178 Chirality : 0.093 0.351 3648 Planarity : 0.013 0.096 3976 Dihedral : 13.711 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 0.01289 / 0.77 (23376) covalent geometry : angle 1.82686 / 1.18 (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 : 0.810 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: 0.6127 time to fit residues: 331.8874 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 : 0.865 ------------------------------------------------------------------------------- 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... 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 = 0.4260 r_free = 0.4260 target = 0.199503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177234 restraints weight = 21932.934| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.25 r_work: 0.3957 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1412 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= 0.136 Angle : 0.571 4.925 31640 Z= 0.315 Chirality : 0.043 0.126 3648 Planarity : 0.004 0.039 3976 Dihedral : 10.082 54.996 3880 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.90 % Allowed : 8.80 % Favored : 88.30 % 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 : 0.00 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 322 TYR 0.015 0.002 TYR B 348 PHE 0.013 0.001 PHE A 401 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (23376) covalent geometry : angle 0.57139 / 0.32 (31640) hydrogen bonds : bond 0.04708 / 3.15 ( 915) hydrogen bonds : angle 4.82104 / 3.42 ( 2583) Misc. bond : bond 0.00023 / 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 471 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 402 time to evaluate : 0.876 Fit side-chains REVERT: A 1 MET cc_start: 0.5820 (mmp) cc_final: 0.5417 (mmp) REVERT: A 256 ASP cc_start: 0.7853 (m-30) cc_final: 0.7417 (m-30) REVERT: A 335 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6562 (mp0) REVERT: A 483 MET cc_start: 0.8593 (tmm) cc_final: 0.8160 (tmm) REVERT: B 75 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: B 256 ASP cc_start: 0.7725 (m-30) cc_final: 0.7210 (m-30) REVERT: B 277 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.5785 (tm-30) REVERT: B 335 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6674 (mp0) REVERT: B 420 MET cc_start: 0.7404 (ptm) cc_final: 0.7010 (ptt) REVERT: B 483 MET cc_start: 0.8597 (tmm) cc_final: 0.8370 (tmm) REVERT: C 1 MET cc_start: 0.5849 (mmp) cc_final: 0.5415 (mmp) REVERT: C 98 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: C 256 ASP cc_start: 0.7904 (m-30) cc_final: 0.7660 (m-30) REVERT: C 420 MET cc_start: 0.7281 (ptm) cc_final: 0.6834 (ptt) REVERT: C 483 MET cc_start: 0.8608 (tmm) cc_final: 0.8183 (tmm) REVERT: D 75 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: D 238 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.6130 (mttt) REVERT: D 255 ASP cc_start: 0.7734 (p0) cc_final: 0.7390 (p0) REVERT: D 277 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.5980 (tm-30) REVERT: D 448 GLN cc_start: 0.7596 (pt0) cc_final: 0.7388 (pt0) REVERT: D 483 MET cc_start: 0.8588 (tmm) cc_final: 0.8361 (tmm) REVERT: E 98 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: E 255 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7281 (p0) REVERT: E 256 ASP cc_start: 0.7801 (m-30) cc_final: 0.7317 (m-30) REVERT: E 335 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6709 (mp0) REVERT: E 483 MET cc_start: 0.8583 (tmm) cc_final: 0.8346 (tmm) REVERT: F 1 MET cc_start: 0.5899 (mmp) cc_final: 0.5352 (tpp) REVERT: F 98 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7230 (mm-30) REVERT: F 255 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7269 (p0) REVERT: F 256 ASP cc_start: 0.7719 (m-30) cc_final: 0.7259 (m-30) REVERT: F 335 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6608 (mp0) REVERT: F 483 MET cc_start: 0.8614 (tmm) cc_final: 0.8384 (tmm) REVERT: G 1 MET cc_start: 0.5918 (mmp) cc_final: 0.5494 (mmp) REVERT: G 75 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: G 98 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: G 238 LYS cc_start: 0.6647 (OUTLIER) cc_final: 0.6319 (mttt) REVERT: G 256 ASP cc_start: 0.7749 (m-30) cc_final: 0.7367 (m-30) REVERT: G 277 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.5817 (tm-30) REVERT: G 335 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6683 (mp0) REVERT: G 448 GLN cc_start: 0.7437 (pt0) cc_final: 0.7223 (pt0) REVERT: G 483 MET cc_start: 0.8587 (tmm) cc_final: 0.8154 (tmm) REVERT: G 498 GLN cc_start: 0.7336 (mt0) cc_final: 0.7136 (mt0) REVERT: H 1 MET cc_start: 0.6002 (mmp) cc_final: 0.5701 (mmp) REVERT: H 75 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: H 98 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: H 256 ASP cc_start: 0.7810 (m-30) cc_final: 0.7402 (m-30) REVERT: H 335 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6544 (mp0) REVERT: H 420 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6912 (ptt) REVERT: H 483 MET cc_start: 0.8610 (tmm) cc_final: 0.8389 (tmm) outliers start: 69 outliers final: 22 residues processed: 444 average time/residue: 0.6329 time to fit residues: 321.7742 Evaluate side-chains 411 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 372 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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: 0.0000 chunk 194 optimal weight: 5.9990 chunk 103 optimal weight: 0.0010 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: 10.0000 chunk 112 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4241 r_free = 0.4241 target = 0.197343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175401 restraints weight = 22045.255| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.25 r_work: 0.3936 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23384 Z= 0.167 Angle : 0.620 4.853 31640 Z= 0.340 Chirality : 0.045 0.137 3648 Planarity : 0.004 0.041 3976 Dihedral : 10.047 53.627 3868 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.79 % Allowed : 9.43 % Favored : 86.78 % 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: 0.46 (0.15), residues: 2952 helix: 1.38 (0.16), residues: 1144 sheet: -0.66 (0.25), residues: 416 loop : -0.20 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 105 TYR 0.016 0.002 TYR B 348 PHE 0.014 0.002 PHE A 401 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (23376) covalent geometry : angle 0.61981 / 0.34 (31640) hydrogen bonds : bond 0.05375 / 3.60 ( 915) hydrogen bonds : angle 4.82465 / 3.42 ( 2583) Misc. bond : bond 0.00059 / 0.03 ( 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 468 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 378 time to evaluate : 0.841 Fit side-chains REVERT: A 1 MET cc_start: 0.5922 (mmp) cc_final: 0.5527 (mmp) REVERT: A 98 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: A 256 ASP cc_start: 0.7827 (m-30) cc_final: 0.7403 (m-30) REVERT: A 277 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.6323 (tp40) REVERT: A 335 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6567 (mp0) REVERT: A 420 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7037 (ptt) REVERT: A 483 MET cc_start: 0.8589 (tmm) cc_final: 0.8008 (tmm) REVERT: B 75 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: B 98 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: B 256 ASP cc_start: 0.7727 (m-30) cc_final: 0.7230 (m-30) REVERT: B 277 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.6011 (tm-30) REVERT: B 335 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6652 (mp0) REVERT: B 420 MET cc_start: 0.7444 (ptm) cc_final: 0.7238 (ptt) REVERT: B 483 MET cc_start: 0.8585 (tmm) cc_final: 0.8012 (tmm) REVERT: C 256 ASP cc_start: 0.7870 (m-30) cc_final: 0.7598 (m-30) REVERT: C 277 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.6341 (tp40) REVERT: C 483 MET cc_start: 0.8578 (tmm) cc_final: 0.7986 (tmm) REVERT: D 75 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: D 98 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: D 255 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7461 (p0) REVERT: D 256 ASP cc_start: 0.7677 (m-30) cc_final: 0.7263 (m-30) REVERT: D 277 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.6121 (tm-30) REVERT: D 483 MET cc_start: 0.8594 (tmm) cc_final: 0.8018 (tmm) REVERT: E 75 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: E 98 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: E 242 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7506 (mttp) REVERT: E 255 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7406 (p0) REVERT: E 256 ASP cc_start: 0.7776 (m-30) cc_final: 0.7256 (m-30) REVERT: E 335 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6644 (mp0) REVERT: E 483 MET cc_start: 0.8577 (tmm) cc_final: 0.7988 (tmm) REVERT: F 1 MET cc_start: 0.5906 (mmp) cc_final: 0.5428 (mmp) REVERT: F 98 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: F 255 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7330 (p0) REVERT: F 256 ASP cc_start: 0.7731 (m-30) cc_final: 0.7229 (m-30) REVERT: F 277 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.6295 (tp40) REVERT: F 335 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6579 (mp0) REVERT: F 483 MET cc_start: 0.8599 (tmm) cc_final: 0.8027 (tmm) REVERT: G 1 MET cc_start: 0.6002 (mmp) cc_final: 0.5579 (mmp) REVERT: G 75 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: G 256 ASP cc_start: 0.7829 (m-30) cc_final: 0.7419 (m-30) REVERT: G 277 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.6268 (tm-30) REVERT: G 483 MET cc_start: 0.8577 (tmm) cc_final: 0.7978 (tmm) REVERT: H 1 MET cc_start: 0.6024 (mmp) cc_final: 0.5701 (mmp) REVERT: H 98 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: H 256 ASP cc_start: 0.7835 (m-30) cc_final: 0.7410 (m-30) REVERT: H 277 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.6283 (tp40) REVERT: H 335 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6546 (mp0) REVERT: H 483 MET cc_start: 0.8605 (tmm) cc_final: 0.8036 (tmm) outliers start: 90 outliers final: 33 residues processed: 444 average time/residue: 0.6499 time to fit residues: 330.9047 Evaluate side-chains 415 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 360 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 245 LEU 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 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 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 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 277 GLN Chi-restraints excluded: chain F residue 345 THR 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 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 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 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: 1.9990 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN B 265 GLN C 243 GLN E 265 GLN F 243 GLN F 265 GLN G 21 GLN G 243 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 = 0.4240 r_free = 0.4240 target = 0.197345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.175487 restraints weight = 22052.814| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.24 r_work: 0.3935 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23384 Z= 0.165 Angle : 0.610 4.861 31640 Z= 0.334 Chirality : 0.045 0.134 3648 Planarity : 0.004 0.045 3976 Dihedral : 10.125 55.173 3868 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.79 % Allowed : 9.93 % Favored : 86.28 % 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: 0.39 (0.15), residues: 2952 helix: 1.36 (0.16), residues: 1144 sheet: -0.67 (0.25), residues: 416 loop : -0.28 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 105 TYR 0.016 0.002 TYR B 348 PHE 0.013 0.002 PHE H 401 HIS 0.002 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (23376) covalent geometry : angle 0.60999 / 0.33 (31640) hydrogen bonds : bond 0.05191 / 3.48 ( 915) hydrogen bonds : angle 4.74097 / 3.37 ( 2583) Misc. bond : bond 0.00048 / 0.02 ( 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 457 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 367 time to evaluate : 0.901 Fit side-chains REVERT: A 1 MET cc_start: 0.5931 (mmp) cc_final: 0.5458 (mmp) REVERT: A 98 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: A 256 ASP cc_start: 0.7817 (m-30) cc_final: 0.7360 (m-30) REVERT: A 277 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.6319 (tp40) REVERT: A 420 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7071 (ptt) REVERT: A 483 MET cc_start: 0.8584 (tmm) cc_final: 0.7972 (tmm) REVERT: B 75 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: B 98 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: B 256 ASP cc_start: 0.7718 (m-30) cc_final: 0.7240 (m-30) REVERT: B 277 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6186 (tm-30) REVERT: B 420 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7170 (ptt) REVERT: B 483 MET cc_start: 0.8577 (tmm) cc_final: 0.7962 (tmm) REVERT: C 98 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: C 256 ASP cc_start: 0.7849 (m-30) cc_final: 0.7576 (m-30) REVERT: C 277 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.6446 (tp40) REVERT: C 455 LYS cc_start: 0.7513 (pttt) cc_final: 0.7219 (ttpp) REVERT: C 483 MET cc_start: 0.8581 (tmm) cc_final: 0.7971 (tmm) REVERT: D 75 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: D 98 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: D 255 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7440 (p0) REVERT: D 256 ASP cc_start: 0.7692 (m-30) cc_final: 0.7292 (m-30) REVERT: D 277 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.6197 (tm-30) REVERT: D 483 MET cc_start: 0.8593 (tmm) cc_final: 0.7980 (tmm) REVERT: E 98 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: E 242 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7476 (mttp) REVERT: E 255 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7408 (p0) REVERT: E 256 ASP cc_start: 0.7759 (m-30) cc_final: 0.7269 (m-30) REVERT: E 277 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.6413 (tm-30) REVERT: E 483 MET cc_start: 0.8562 (tmm) cc_final: 0.7935 (tmm) REVERT: F 1 MET cc_start: 0.6002 (mmp) cc_final: 0.5479 (mmp) REVERT: F 98 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: F 255 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7358 (p0) REVERT: F 256 ASP cc_start: 0.7716 (m-30) cc_final: 0.7229 (m-30) REVERT: F 277 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.6417 (tp40) REVERT: F 483 MET cc_start: 0.8585 (tmm) cc_final: 0.8038 (tmm) REVERT: G 1 MET cc_start: 0.6004 (mmp) cc_final: 0.5577 (mmp) REVERT: G 75 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: G 98 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: G 242 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7505 (mptp) REVERT: G 256 ASP cc_start: 0.7832 (m-30) cc_final: 0.7381 (m-30) REVERT: G 277 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.6240 (tm-30) REVERT: G 483 MET cc_start: 0.8565 (tmm) cc_final: 0.8261 (tmm) REVERT: H 1 MET cc_start: 0.5984 (mmp) cc_final: 0.5665 (mmp) REVERT: H 98 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7157 (mm-30) REVERT: H 256 ASP cc_start: 0.7787 (m-30) cc_final: 0.7365 (m-30) REVERT: H 277 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.6303 (tp40) REVERT: H 483 MET cc_start: 0.8589 (tmm) cc_final: 0.7970 (tmm) outliers start: 90 outliers final: 34 residues processed: 435 average time/residue: 0.6260 time to fit residues: 311.9753 Evaluate side-chains 418 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 359 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 370 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain C residue 63 THR 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 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 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 361 VAL 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 255 optimal weight: 1.9990 chunk 226 optimal weight: 0.0570 chunk 183 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN B 21 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.202185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.180755 restraints weight = 22027.342| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.24 r_work: 0.3996 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3912 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23384 Z= 0.096 Angle : 0.490 5.285 31640 Z= 0.270 Chirality : 0.040 0.128 3648 Planarity : 0.004 0.043 3976 Dihedral : 9.693 57.233 3868 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.42 % Allowed : 9.89 % Favored : 85.69 % 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: 0.77 (0.16), residues: 2952 helix: 1.73 (0.16), residues: 1144 sheet: -0.59 (0.26), residues: 416 loop : -0.07 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 105 TYR 0.014 0.001 TYR H 12 PHE 0.011 0.001 PHE A 401 HIS 0.003 0.000 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (23376) covalent geometry : angle 0.49024 / 0.27 (31640) hydrogen bonds : bond 0.03527 / 2.36 ( 915) hydrogen bonds : angle 4.34807 / 3.09 ( 2583) Misc. bond : bond 0.00007 / 0.00 ( 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 503 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 398 time to evaluate : 0.886 Fit side-chains REVERT: A 1 MET cc_start: 0.5927 (mmp) cc_final: 0.5422 (mmp) REVERT: A 98 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: A 256 ASP cc_start: 0.7766 (m-30) cc_final: 0.7354 (m-30) REVERT: A 420 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.7033 (ptt) REVERT: A 483 MET cc_start: 0.8549 (tmm) cc_final: 0.7897 (tmm) REVERT: B 75 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: B 98 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: B 256 ASP cc_start: 0.7656 (m-30) cc_final: 0.7157 (m-30) REVERT: B 277 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.5731 (tm-30) REVERT: B 483 MET cc_start: 0.8555 (tmm) cc_final: 0.7915 (tmm) REVERT: C 256 ASP cc_start: 0.7804 (m-30) cc_final: 0.7582 (m-30) REVERT: C 483 MET cc_start: 0.8542 (tmm) cc_final: 0.8163 (tmm) REVERT: D 75 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: D 98 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: D 255 ASP cc_start: 0.7675 (p0) cc_final: 0.7409 (p0) REVERT: D 256 ASP cc_start: 0.7649 (m-30) cc_final: 0.7265 (m-30) REVERT: D 277 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.5749 (tm-30) REVERT: D 483 MET cc_start: 0.8556 (tmm) cc_final: 0.7900 (tmm) REVERT: E 75 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: E 98 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: E 255 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7390 (p0) REVERT: E 256 ASP cc_start: 0.7719 (m-30) cc_final: 0.7178 (m-30) REVERT: E 277 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.5469 (tm-30) REVERT: E 483 MET cc_start: 0.8527 (tmm) cc_final: 0.8147 (tmm) REVERT: F 1 MET cc_start: 0.5976 (mmp) cc_final: 0.5459 (mmp) REVERT: F 98 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: F 255 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7491 (p0) REVERT: F 256 ASP cc_start: 0.7699 (m-30) cc_final: 0.7175 (m-30) REVERT: F 335 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6452 (mp0) REVERT: F 483 MET cc_start: 0.8579 (tmm) cc_final: 0.7953 (tmm) REVERT: G 1 MET cc_start: 0.6020 (mmp) cc_final: 0.5704 (mmp) REVERT: G 75 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: G 242 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7498 (mptp) REVERT: G 256 ASP cc_start: 0.7798 (m-30) cc_final: 0.7408 (m-30) REVERT: G 277 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.5775 (tm-30) REVERT: G 483 MET cc_start: 0.8531 (tmm) cc_final: 0.7857 (tmm) REVERT: H 1 MET cc_start: 0.6000 (mmp) cc_final: 0.5702 (mmp) REVERT: H 75 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: H 98 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: H 256 ASP cc_start: 0.7741 (m-30) cc_final: 0.7361 (m-30) REVERT: H 483 MET cc_start: 0.8575 (tmm) cc_final: 0.7939 (tmm) outliers start: 105 outliers final: 36 residues processed: 477 average time/residue: 0.5949 time to fit residues: 327.6808 Evaluate side-chains 415 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 361 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 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 345 THR Chi-restraints excluded: chain C residue 361 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 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 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 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 406 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 66 optimal weight: 0.0970 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 265 GLN E 265 GLN F 265 GLN G 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.198217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.176417 restraints weight = 21915.334| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.23 r_work: 0.3946 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23384 Z= 0.154 Angle : 0.587 5.183 31640 Z= 0.321 Chirality : 0.044 0.135 3648 Planarity : 0.004 0.042 3976 Dihedral : 10.050 56.849 3868 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.96 % Allowed : 10.61 % Favored : 85.44 % 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: 0.57 (0.15), residues: 2952 helix: 1.53 (0.16), residues: 1144 sheet: -0.69 (0.26), residues: 416 loop : -0.16 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 105 TYR 0.016 0.002 TYR B 348 PHE 0.014 0.002 PHE A 401 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (23376) covalent geometry : angle 0.58707 / 0.32 (31640) hydrogen bonds : bond 0.04921 / 3.29 ( 915) hydrogen bonds : angle 4.58229 / 3.25 ( 2583) Misc. bond : bond 0.00041 / 0.02 ( 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 465 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 371 time to evaluate : 0.875 Fit side-chains REVERT: A 1 MET cc_start: 0.5921 (mmp) cc_final: 0.5408 (mmp) REVERT: A 98 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: A 256 ASP cc_start: 0.7852 (m-30) cc_final: 0.7364 (m-30) REVERT: A 277 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.5538 (tm-30) REVERT: A 420 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7208 (ptt) REVERT: A 483 MET cc_start: 0.8578 (tmm) cc_final: 0.7958 (tmm) REVERT: B 75 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: B 98 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7167 (mm-30) REVERT: B 256 ASP cc_start: 0.7674 (m-30) cc_final: 0.7201 (m-30) REVERT: B 277 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.6091 (tm-30) REVERT: B 335 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6535 (mp0) REVERT: B 483 MET cc_start: 0.8582 (tmm) cc_final: 0.7980 (tmm) REVERT: C 98 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: C 256 ASP cc_start: 0.7840 (m-30) cc_final: 0.7549 (m-30) REVERT: C 277 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.5524 (tm-30) REVERT: C 455 LYS cc_start: 0.7492 (pttt) cc_final: 0.7169 (ttpp) REVERT: C 483 MET cc_start: 0.8581 (tmm) cc_final: 0.8290 (tmm) REVERT: D 75 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: D 98 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: D 255 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7463 (p0) REVERT: D 256 ASP cc_start: 0.7675 (m-30) cc_final: 0.7283 (m-30) REVERT: D 277 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.6109 (tm-30) REVERT: D 483 MET cc_start: 0.8607 (tmm) cc_final: 0.8023 (tmm) REVERT: E 75 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: E 98 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: E 255 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7465 (p0) REVERT: E 256 ASP cc_start: 0.7743 (m-30) cc_final: 0.7213 (m-30) REVERT: E 277 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.5601 (tm-30) REVERT: E 483 MET cc_start: 0.8576 (tmm) cc_final: 0.7966 (tmm) REVERT: F 1 MET cc_start: 0.5933 (mmp) cc_final: 0.5422 (mmp) REVERT: F 98 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: F 255 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7412 (p0) REVERT: F 256 ASP cc_start: 0.7717 (m-30) cc_final: 0.7249 (m-30) REVERT: F 277 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.5465 (tm-30) REVERT: F 483 MET cc_start: 0.8584 (tmm) cc_final: 0.8094 (tmm) REVERT: G 1 MET cc_start: 0.6005 (mmp) cc_final: 0.5598 (mmp) REVERT: G 75 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: G 98 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: G 242 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7535 (mptp) REVERT: G 256 ASP cc_start: 0.7845 (m-30) cc_final: 0.7394 (m-30) REVERT: G 277 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.6220 (tm-30) REVERT: G 483 MET cc_start: 0.8590 (tmm) cc_final: 0.7985 (tmm) REVERT: H 1 MET cc_start: 0.5966 (mmp) cc_final: 0.5567 (mmp) REVERT: H 75 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: H 98 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: H 256 ASP cc_start: 0.7819 (m-30) cc_final: 0.7384 (m-30) REVERT: H 277 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.5472 (tm-30) REVERT: H 483 MET cc_start: 0.8602 (tmm) cc_final: 0.8008 (tmm) outliers start: 94 outliers final: 44 residues processed: 447 average time/residue: 0.6432 time to fit residues: 329.0756 Evaluate side-chains 431 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 362 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 281 ILE 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 406 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 281 ILE 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 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 281 ILE 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 281 ILE 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 406 ILE 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 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 281 ILE 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 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 406 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 41 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 293 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN B 21 GLN B 478 GLN C 21 GLN C 265 GLN D 21 GLN D 265 GLN E 21 GLN E 265 GLN F 21 GLN F 265 GLN G 21 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.199222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.177468 restraints weight = 21975.264| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.23 r_work: 0.3959 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1825 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= 0.128 Angle : 0.544 6.090 31640 Z= 0.299 Chirality : 0.042 0.130 3648 Planarity : 0.004 0.044 3976 Dihedral : 9.996 57.013 3868 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.83 % Allowed : 10.73 % Favored : 85.44 % 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: 0.59 (0.15), residues: 2952 helix: 1.57 (0.16), residues: 1144 sheet: -0.72 (0.26), residues: 416 loop : -0.17 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 105 TYR 0.014 0.002 TYR H 12 PHE 0.013 0.001 PHE H 401 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (23376) covalent geometry : angle 0.54364 / 0.30 (31640) hydrogen bonds : bond 0.04387 / 2.94 ( 915) hydrogen bonds : angle 4.46140 / 3.16 ( 2583) Misc. bond : bond 0.00022 / 0.01 ( 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: 91 poor density : 369 time to evaluate : 0.870 Fit side-chains REVERT: A 1 MET cc_start: 0.5941 (mmp) cc_final: 0.5435 (mmp) REVERT: A 98 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: A 256 ASP cc_start: 0.7809 (m-30) cc_final: 0.7312 (m-30) REVERT: A 277 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.5490 (tm-30) REVERT: A 420 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7084 (ptt) REVERT: A 483 MET cc_start: 0.8568 (tmm) cc_final: 0.7916 (tmm) REVERT: A 491 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: B 75 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: B 98 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: B 256 ASP cc_start: 0.7668 (m-30) cc_final: 0.7179 (m-30) REVERT: B 277 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.6004 (tm-30) REVERT: B 483 MET cc_start: 0.8576 (tmm) cc_final: 0.7916 (tmm) REVERT: C 98 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: C 256 ASP cc_start: 0.7813 (m-30) cc_final: 0.7554 (m-30) REVERT: C 277 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.5478 (tm-30) REVERT: C 455 LYS cc_start: 0.7446 (pttt) cc_final: 0.7117 (ttpp) REVERT: C 483 MET cc_start: 0.8580 (tmm) cc_final: 0.7937 (tmm) REVERT: D 75 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: D 98 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7107 (mm-30) REVERT: D 255 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7444 (p0) REVERT: D 256 ASP cc_start: 0.7659 (m-30) cc_final: 0.7283 (m-30) REVERT: D 277 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.6079 (tm-30) REVERT: D 483 MET cc_start: 0.8604 (tmm) cc_final: 0.8015 (tmm) REVERT: E 75 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: E 98 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: E 255 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7456 (p0) REVERT: E 256 ASP cc_start: 0.7722 (m-30) cc_final: 0.7206 (m-30) REVERT: E 277 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.5634 (tm-30) REVERT: E 483 MET cc_start: 0.8578 (tmm) cc_final: 0.7940 (tmm) REVERT: E 491 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: F 1 MET cc_start: 0.5920 (mmp) cc_final: 0.5409 (mmp) REVERT: F 98 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7168 (mm-30) REVERT: F 255 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7406 (p0) REVERT: F 256 ASP cc_start: 0.7695 (m-30) cc_final: 0.7202 (m-30) REVERT: F 277 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.5429 (tm-30) REVERT: F 483 MET cc_start: 0.8578 (tmm) cc_final: 0.7940 (tmm) REVERT: G 1 MET cc_start: 0.6026 (mmp) cc_final: 0.5622 (mmp) REVERT: G 75 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: G 98 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7050 (mm-30) REVERT: G 242 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7524 (mptp) REVERT: G 255 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7229 (p0) REVERT: G 256 ASP cc_start: 0.7824 (m-30) cc_final: 0.7428 (m-30) REVERT: G 277 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.6121 (tm-30) REVERT: G 483 MET cc_start: 0.8569 (tmm) cc_final: 0.7952 (tmm) REVERT: H 1 MET cc_start: 0.5968 (mmp) cc_final: 0.5570 (mmp) REVERT: H 98 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: H 256 ASP cc_start: 0.7788 (m-30) cc_final: 0.7374 (m-30) REVERT: H 277 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.5416 (tm-30) REVERT: H 335 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6591 (mp0) REVERT: H 483 MET cc_start: 0.8601 (tmm) cc_final: 0.8001 (tmm) REVERT: H 491 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7773 (tt0) outliers start: 91 outliers final: 47 residues processed: 436 average time/residue: 0.6430 time to fit residues: 321.5037 Evaluate side-chains 429 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 354 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 A residue 406 ILE Chi-restraints excluded: chain A residue 420 MET 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 98 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 281 ILE 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 406 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 281 ILE 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 406 ILE 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 281 ILE 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 448 GLN 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 281 ILE 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 406 ILE 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 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 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 281 ILE 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 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.0970 chunk 123 optimal weight: 0.1980 chunk 228 optimal weight: 0.0870 chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN B 48 GLN B 478 GLN C 265 GLN D 265 GLN E 265 GLN G 21 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 = 0.4307 r_free = 0.4307 target = 0.204295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.182973 restraints weight = 22022.856| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.23 r_work: 0.4023 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23384 Z= 0.087 Angle : 0.465 6.667 31640 Z= 0.254 Chirality : 0.040 0.126 3648 Planarity : 0.003 0.046 3976 Dihedral : 9.560 59.036 3868 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.32 % Allowed : 12.12 % Favored : 84.55 % 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: 0.97 (0.16), residues: 2952 helix: 1.85 (0.16), residues: 1136 sheet: -0.58 (0.25), residues: 424 loop : 0.14 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 105 TYR 0.013 0.001 TYR H 12 PHE 0.011 0.001 PHE H 401 HIS 0.003 0.000 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 (23376) covalent geometry : angle 0.46468 / 0.25 (31640) hydrogen bonds : bond 0.03067 / 2.05 ( 915) hydrogen bonds : angle 4.15640 / 2.95 ( 2583) Misc. bond : bond 0.00006 / 0.00 ( 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 462 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 383 time to evaluate : 0.883 Fit side-chains REVERT: A 1 MET cc_start: 0.5858 (mmp) cc_final: 0.5347 (mmp) REVERT: A 98 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: A 256 ASP cc_start: 0.7717 (m-30) cc_final: 0.7373 (m-30) REVERT: A 277 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.5963 (tm-30) REVERT: A 420 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6920 (ptt) REVERT: A 483 MET cc_start: 0.8518 (tmm) cc_final: 0.7748 (tmm) REVERT: B 75 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: B 256 ASP cc_start: 0.7662 (m-30) cc_final: 0.7154 (m-30) REVERT: B 277 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.5641 (tm-30) REVERT: B 483 MET cc_start: 0.8530 (tmm) cc_final: 0.7802 (tmm) REVERT: C 256 ASP cc_start: 0.7782 (m-30) cc_final: 0.7500 (m-30) REVERT: C 277 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.5186 (tm-30) REVERT: C 483 MET cc_start: 0.8510 (tmm) cc_final: 0.7730 (tmm) REVERT: D 75 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: D 242 LYS cc_start: 0.7704 (mtpp) cc_final: 0.7494 (mptp) REVERT: D 255 ASP cc_start: 0.7657 (p0) cc_final: 0.7382 (p0) REVERT: D 256 ASP cc_start: 0.7640 (m-30) cc_final: 0.7218 (m-30) REVERT: D 277 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.5642 (tm-30) REVERT: D 483 MET cc_start: 0.8499 (tmm) cc_final: 0.7993 (tmm) REVERT: E 75 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: E 255 ASP cc_start: 0.7626 (p0) cc_final: 0.7392 (p0) REVERT: E 256 ASP cc_start: 0.7738 (m-30) cc_final: 0.7218 (m-30) REVERT: E 483 MET cc_start: 0.8506 (tmm) cc_final: 0.8129 (tmm) REVERT: F 1 MET cc_start: 0.5944 (mmp) cc_final: 0.5437 (mmp) REVERT: F 98 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7119 (mm-30) REVERT: F 255 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7435 (p0) REVERT: F 256 ASP cc_start: 0.7694 (m-30) cc_final: 0.7198 (m-30) REVERT: F 277 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.5928 (tm-30) REVERT: F 483 MET cc_start: 0.8542 (tmm) cc_final: 0.7812 (tmm) REVERT: G 1 MET cc_start: 0.6029 (mmp) cc_final: 0.5621 (mmp) REVERT: G 75 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7758 (mt-10) REVERT: G 256 ASP cc_start: 0.7773 (m-30) cc_final: 0.7458 (m-30) REVERT: G 277 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.5695 (tm-30) REVERT: G 483 MET cc_start: 0.8460 (tmm) cc_final: 0.7927 (tmm) REVERT: H 1 MET cc_start: 0.5953 (mmp) cc_final: 0.5659 (mmp) REVERT: H 256 ASP cc_start: 0.7725 (m-30) cc_final: 0.7399 (m-30) REVERT: H 277 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.5906 (tm-30) outliers start: 79 outliers final: 31 residues processed: 444 average time/residue: 0.6267 time to fit residues: 320.5241 Evaluate side-chains 421 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 375 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 420 MET 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 406 ILE Chi-restraints excluded: chain C residue 63 THR 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 406 ILE 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 E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 406 ILE 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 406 ILE 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 406 ILE Chi-restraints excluded: chain H residue 63 THR 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 406 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 2 optimal weight: 0.0870 chunk 141 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN B 478 GLN D 265 GLN D 478 GLN E 296 ASN F 265 GLN F 296 ASN G 478 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.199885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178006 restraints weight = 21774.111| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 1.25 r_work: 0.3969 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23384 Z= 0.123 Angle : 0.531 5.845 31640 Z= 0.290 Chirality : 0.042 0.127 3648 Planarity : 0.004 0.045 3976 Dihedral : 9.839 58.263 3866 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.74 % Allowed : 13.38 % Favored : 83.88 % 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: 0.74 (0.16), residues: 2952 helix: 1.72 (0.16), residues: 1144 sheet: -0.91 (0.25), residues: 416 loop : 0.01 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 105 TYR 0.015 0.002 TYR B 348 PHE 0.014 0.001 PHE A 401 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (23376) covalent geometry : angle 0.53063 / 0.29 (31640) hydrogen bonds : bond 0.04137 / 2.77 ( 915) hydrogen bonds : angle 4.33396 / 3.07 ( 2583) Misc. bond : bond 0.00014 / 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 440 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 375 time to evaluate : 0.872 Fit side-chains REVERT: A 1 MET cc_start: 0.5909 (mmp) cc_final: 0.5389 (mmp) REVERT: A 98 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: A 256 ASP cc_start: 0.7802 (m-30) cc_final: 0.7440 (m-30) REVERT: A 277 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.5415 (tm-30) REVERT: A 420 MET cc_start: 0.7254 (ptm) cc_final: 0.7051 (ptt) REVERT: A 483 MET cc_start: 0.8570 (tmm) cc_final: 0.7859 (tmm) REVERT: A 491 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: B 75 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 256 ASP cc_start: 0.7642 (m-30) cc_final: 0.7180 (m-30) REVERT: B 277 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.5796 (tm-30) REVERT: B 483 MET cc_start: 0.8579 (tmm) cc_final: 0.7901 (tmm) REVERT: B 491 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: C 256 ASP cc_start: 0.7830 (m-30) cc_final: 0.7582 (m-30) REVERT: C 277 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.5402 (tm-30) REVERT: C 455 LYS cc_start: 0.7435 (pttt) cc_final: 0.7096 (ttpp) REVERT: C 483 MET cc_start: 0.8584 (tmm) cc_final: 0.7882 (tmm) REVERT: C 491 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: D 75 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: D 98 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: D 255 ASP cc_start: 0.7662 (p0) cc_final: 0.7394 (p0) REVERT: D 256 ASP cc_start: 0.7574 (m-30) cc_final: 0.7200 (m-30) REVERT: D 277 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.5855 (tm-30) REVERT: D 483 MET cc_start: 0.8574 (tmm) cc_final: 0.7950 (tmm) REVERT: D 491 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: E 75 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: E 255 ASP cc_start: 0.7668 (p0) cc_final: 0.7424 (p0) REVERT: E 256 ASP cc_start: 0.7725 (m-30) cc_final: 0.7231 (m-30) REVERT: E 277 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.5441 (tm-30) REVERT: E 483 MET cc_start: 0.8571 (tmm) cc_final: 0.7858 (tmm) REVERT: E 491 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: F 1 MET cc_start: 0.6021 (mmp) cc_final: 0.5521 (mmp) REVERT: F 98 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: F 255 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7378 (p0) REVERT: F 256 ASP cc_start: 0.7629 (m-30) cc_final: 0.7149 (m-30) REVERT: F 277 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.5501 (tm-30) REVERT: F 483 MET cc_start: 0.8604 (tmm) cc_final: 0.7927 (tmm) REVERT: F 491 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: G 1 MET cc_start: 0.5980 (mmp) cc_final: 0.5557 (mmp) REVERT: G 75 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: G 256 ASP cc_start: 0.7828 (m-30) cc_final: 0.7458 (m-30) REVERT: G 277 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.5850 (tm-30) REVERT: G 483 MET cc_start: 0.8553 (tmm) cc_final: 0.7921 (tmm) REVERT: G 491 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: H 1 MET cc_start: 0.6052 (mmp) cc_final: 0.5661 (mmp) REVERT: H 98 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: H 256 ASP cc_start: 0.7696 (m-30) cc_final: 0.7286 (m-30) REVERT: H 277 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.5475 (tm-30) REVERT: H 491 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7780 (tt0) outliers start: 65 outliers final: 32 residues processed: 420 average time/residue: 0.6477 time to fit residues: 310.8646 Evaluate side-chains 430 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 373 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 406 ILE 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 491 GLU Chi-restraints excluded: chain C residue 63 THR 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 406 ILE 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 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 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 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 406 ILE 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 406 ILE 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 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 406 ILE 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: 9.9990 chunk 94 optimal weight: 0.0170 chunk 134 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 246 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN B 21 GLN B 478 GLN C 265 GLN D 21 GLN D 265 GLN D 478 GLN F 296 ASN G 21 GLN G 478 GLN H 21 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.176930 restraints weight = 21829.397| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.25 r_work: 0.3956 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23384 Z= 0.133 Angle : 0.553 6.023 31640 Z= 0.303 Chirality : 0.043 0.138 3648 Planarity : 0.004 0.044 3976 Dihedral : 10.028 59.247 3866 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.69 % Allowed : 13.30 % Favored : 84.01 % 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: 0.60 (0.15), residues: 2952 helix: 1.64 (0.16), residues: 1144 sheet: -0.94 (0.25), residues: 416 loop : -0.12 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 105 TYR 0.015 0.002 TYR H 12 PHE 0.013 0.002 PHE H 401 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (23376) covalent geometry : angle 0.55287 / 0.30 (31640) hydrogen bonds : bond 0.04424 / 2.96 ( 915) hydrogen bonds : angle 4.40002 / 3.12 ( 2583) Misc. bond : bond 0.00024 / 0.01 ( 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 426 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 362 time to evaluate : 0.888 Fit side-chains REVERT: A 1 MET cc_start: 0.5859 (mmp) cc_final: 0.5352 (mmp) REVERT: A 98 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: A 256 ASP cc_start: 0.7823 (m-30) cc_final: 0.7340 (m-30) REVERT: A 277 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.5436 (tm-30) REVERT: A 420 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7084 (ptt) REVERT: A 483 MET cc_start: 0.8596 (tmm) cc_final: 0.7915 (tmm) REVERT: B 75 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: B 98 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: B 256 ASP cc_start: 0.7644 (m-30) cc_final: 0.7190 (m-30) REVERT: B 277 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.6090 (tm-30) REVERT: B 483 MET cc_start: 0.8597 (tmm) cc_final: 0.7935 (tmm) REVERT: C 98 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: C 256 ASP cc_start: 0.7865 (m-30) cc_final: 0.7583 (m-30) REVERT: C 277 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.5432 (tm-30) REVERT: C 455 LYS cc_start: 0.7472 (pttt) cc_final: 0.7130 (ttpp) REVERT: C 483 MET cc_start: 0.8604 (tmm) cc_final: 0.7925 (tmm) REVERT: D 75 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: D 98 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: D 255 ASP cc_start: 0.7669 (p0) cc_final: 0.7399 (p0) REVERT: D 256 ASP cc_start: 0.7579 (m-30) cc_final: 0.7241 (m-30) REVERT: D 277 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.6147 (tm-30) REVERT: D 483 MET cc_start: 0.8558 (tmm) cc_final: 0.7914 (tmm) REVERT: E 75 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: E 255 ASP cc_start: 0.7693 (p0) cc_final: 0.7449 (p0) REVERT: E 256 ASP cc_start: 0.7737 (m-30) cc_final: 0.7253 (m-30) REVERT: E 277 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.5795 (tm-30) REVERT: E 483 MET cc_start: 0.8593 (tmm) cc_final: 0.7902 (tmm) REVERT: E 491 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: F 1 MET cc_start: 0.6078 (mmp) cc_final: 0.5608 (mmp) REVERT: F 98 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: F 255 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7436 (p0) REVERT: F 256 ASP cc_start: 0.7644 (m-30) cc_final: 0.7150 (m-30) REVERT: F 277 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.5515 (tm-30) REVERT: F 483 MET cc_start: 0.8627 (tmm) cc_final: 0.7972 (tmm) REVERT: G 1 MET cc_start: 0.6010 (mmp) cc_final: 0.5607 (mmp) REVERT: G 75 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: G 98 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: G 256 ASP cc_start: 0.7836 (m-30) cc_final: 0.7438 (m-30) REVERT: G 277 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.6031 (tm-30) REVERT: H 1 MET cc_start: 0.6066 (mmp) cc_final: 0.5690 (mmp) REVERT: H 98 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: H 256 ASP cc_start: 0.7734 (m-30) cc_final: 0.7283 (m-30) REVERT: H 277 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.5503 (tm-30) REVERT: H 491 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7792 (tt0) outliers start: 64 outliers final: 33 residues processed: 410 average time/residue: 0.6559 time to fit residues: 307.5154 Evaluate side-chains 418 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 362 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 406 ILE 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 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 63 THR 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 406 ILE 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 E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU 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 406 ILE 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 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 361 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 406 ILE 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 16 optimal weight: 0.0670 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 251 optimal weight: 0.3980 chunk 192 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN B 21 GLN B 478 GLN C 265 GLN D 21 GLN D 265 GLN D 478 GLN F 296 ASN G 478 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.200969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.179240 restraints weight = 21768.477| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.24 r_work: 0.3984 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23384 Z= 0.105 Angle : 0.500 5.825 31640 Z= 0.275 Chirality : 0.041 0.128 3648 Planarity : 0.003 0.043 3976 Dihedral : 9.840 59.368 3866 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.53 % Allowed : 13.51 % Favored : 83.96 % 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: 0.74 (0.16), residues: 2952 helix: 1.71 (0.16), residues: 1144 sheet: -0.81 (0.25), residues: 424 loop : -0.01 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 105 TYR 0.014 0.002 TYR A 12 PHE 0.013 0.001 PHE A 401 HIS 0.003 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (23376) covalent geometry : angle 0.50004 / 0.27 (31640) hydrogen bonds : bond 0.03719 / 2.49 ( 915) hydrogen bonds : angle 4.25803 / 3.02 ( 2583) Misc. bond : bond 0.00013 / 0.01 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10134.55 seconds wall clock time: 172 minutes 58.45 seconds (10378.45 seconds total)