Starting phenix.real_space_refine on Fri Feb 6 06:11:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9muc_48628/02_2026/9muc_48628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9muc_48628/02_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_48628/02_2026/9muc_48628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9muc_48628/02_2026/9muc_48628.map" model { file = "/net/cci-nas-00/data/ceres_data/9muc_48628/02_2026/9muc_48628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9muc_48628/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22984 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "C" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "D" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "E" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "F" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "G" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "H" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 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: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 5.39, per 1000 atoms: 0.23 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: 1.80 Conformation dependent library (CDL) restraints added in 702.7 milliseconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 41.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 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: 3.72 Time building geometry restraints manager: 2.41 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: 25250 2.22 - 4.44: 5751 4.44 - 6.65: 585 6.65 - 8.87: 38 8.87 - 11.09: 16 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 - 22.65: 13320 22.65 - 45.30: 742 45.30 - 67.96: 111 67.96 - 90.61: 20 90.61 - 113.26: 7 Dihedral angle restraints: 14200 sinusoidal: 5728 harmonic: 8472 Sorted by residual: dihedral pdb=" C5' IMP F 601 " pdb=" O5' IMP F 601 " pdb=" P IMP F 601 " pdb=" O2P IMP F 601 " ideal model delta sinusoidal sigma weight residual -168.07 -54.81 -113.26 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" C5' IMP B 601 " pdb=" O5' IMP B 601 " pdb=" P IMP B 601 " pdb=" O2P IMP B 601 " ideal model delta sinusoidal sigma weight residual -168.07 -56.02 -112.04 1 2.00e+01 2.50e-03 3.30e+01 dihedral pdb=" C5' IMP H 601 " pdb=" O5' IMP H 601 " pdb=" P IMP H 601 " pdb=" O2P IMP H 601 " ideal model delta sinusoidal sigma weight residual -168.07 -56.05 -112.02 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 14197 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=" 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=" CB TYR G 400 " 0.114 2.00e-02 2.50e+03 6.43e-02 8.28e+01 pdb=" CG TYR G 400 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR G 400 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR G 400 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR G 400 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR G 400 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR G 400 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 400 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP H 601 " 0.112 2.00e-02 2.50e+03 5.67e-02 8.03e+01 pdb=" C2 IMP H 601 " -0.021 2.00e-02 2.50e+03 pdb=" C4 IMP H 601 " -0.071 2.00e-02 2.50e+03 pdb=" C5 IMP H 601 " -0.018 2.00e-02 2.50e+03 pdb=" C6 IMP H 601 " 0.067 2.00e-02 2.50e+03 pdb=" C8 IMP H 601 " -0.004 2.00e-02 2.50e+03 pdb=" N1 IMP H 601 " 0.059 2.00e-02 2.50e+03 pdb=" N3 IMP H 601 " -0.061 2.00e-02 2.50e+03 pdb=" N7 IMP H 601 " -0.029 2.00e-02 2.50e+03 pdb=" N9 IMP H 601 " -0.035 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: 0.01 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: 1.640 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.490 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.529 23384 Z= 1.162 Angle : 1.822 11.090 31640 Z= 1.177 Chirality : 0.093 0.351 3648 Planarity : 0.013 0.096 3976 Dihedral : 14.062 113.259 8824 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 covalent geometry : bond 0.01294 (23376) covalent geometry : angle 1.82181 (31640) hydrogen bonds : bond 0.18847 ( 915) hydrogen bonds : angle 6.21233 ( 2583) Misc. bond : bond 0.46945 ( 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 : 0.865 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: 0.5692 time to fit residues: 307.5844 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 : 0.721 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN B 21 GLN B 265 GLN C 21 GLN C 243 GLN C 265 GLN D 21 GLN E 21 GLN E 243 GLN F 21 GLN F 243 GLN G 21 GLN G 243 GLN H 21 GLN H 243 GLN H 265 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.199529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177245 restraints weight = 21935.111| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.25 r_work: 0.3958 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23384 Z= 0.135 Angle : 0.571 4.790 31640 Z= 0.314 Chirality : 0.043 0.127 3648 Planarity : 0.004 0.039 3976 Dihedral : 10.151 66.095 3752 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.78 % Allowed : 8.92 % 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: 1.52 (0.16), residues: 1144 sheet: -0.67 (0.25), residues: 432 loop : 0.01 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 322 TYR 0.014 0.002 TYR G 348 PHE 0.013 0.002 PHE A 401 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00289 (23376) covalent geometry : angle 0.57054 (31640) hydrogen bonds : bond 0.04727 ( 915) hydrogen bonds : angle 4.81807 ( 2583) Misc. bond : bond 0.00055 ( 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 467 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 401 time to evaluate : 0.801 Fit side-chains REVERT: A 1 MET cc_start: 0.5772 (mmp) cc_final: 0.5370 (mmp) REVERT: A 256 ASP cc_start: 0.7858 (m-30) cc_final: 0.7404 (m-30) REVERT: A 335 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6553 (mp0) REVERT: A 483 MET cc_start: 0.8607 (tmm) cc_final: 0.8172 (tmm) REVERT: B 75 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: B 256 ASP cc_start: 0.7742 (m-30) cc_final: 0.7210 (m-30) REVERT: B 277 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.5791 (tm-30) REVERT: B 335 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6663 (mp0) REVERT: B 420 MET cc_start: 0.7398 (ptm) cc_final: 0.6999 (ptt) REVERT: B 483 MET cc_start: 0.8597 (tmm) cc_final: 0.8356 (tmm) REVERT: C 1 MET cc_start: 0.5795 (mmp) cc_final: 0.5352 (mmp) REVERT: C 98 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: C 256 ASP cc_start: 0.7915 (m-30) cc_final: 0.7660 (m-30) REVERT: C 420 MET cc_start: 0.7261 (ptm) cc_final: 0.6806 (ptt) REVERT: C 483 MET cc_start: 0.8613 (tmm) cc_final: 0.8185 (tmm) REVERT: D 75 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: D 255 ASP cc_start: 0.7722 (p0) cc_final: 0.7465 (p0) REVERT: D 256 ASP cc_start: 0.7630 (m-30) cc_final: 0.7280 (m-30) REVERT: D 277 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.5810 (tm-30) REVERT: D 483 MET cc_start: 0.8596 (tmm) cc_final: 0.8359 (tmm) REVERT: E 98 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7130 (mm-30) REVERT: E 255 ASP cc_start: 0.7692 (p0) cc_final: 0.7304 (p0) REVERT: E 256 ASP cc_start: 0.7822 (m-30) cc_final: 0.7316 (m-30) REVERT: E 335 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6675 (mp0) REVERT: E 483 MET cc_start: 0.8597 (tmm) cc_final: 0.8181 (tmm) REVERT: F 1 MET cc_start: 0.5855 (mmp) cc_final: 0.5384 (tpp) REVERT: F 98 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: F 255 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7250 (p0) REVERT: F 256 ASP cc_start: 0.7732 (m-30) cc_final: 0.7253 (m-30) REVERT: F 335 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6585 (mp0) REVERT: F 483 MET cc_start: 0.8618 (tmm) cc_final: 0.8217 (tmm) REVERT: G 75 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: G 98 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: G 256 ASP cc_start: 0.7760 (m-30) cc_final: 0.7379 (m-30) REVERT: G 277 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.5806 (tm-30) REVERT: G 335 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6662 (mp0) REVERT: G 448 GLN cc_start: 0.7419 (pt0) cc_final: 0.7196 (pt0) REVERT: G 483 MET cc_start: 0.8593 (tmm) cc_final: 0.8159 (tmm) REVERT: G 498 GLN cc_start: 0.7306 (mt0) cc_final: 0.7093 (mt0) REVERT: H 1 MET cc_start: 0.5952 (mmp) cc_final: 0.5650 (mmp) REVERT: H 98 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: H 256 ASP cc_start: 0.7826 (m-30) cc_final: 0.7404 (m-30) REVERT: H 335 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6531 (mp0) REVERT: H 420 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7200 (ptt) REVERT: H 483 MET cc_start: 0.8616 (tmm) cc_final: 0.8382 (tmm) outliers start: 66 outliers final: 22 residues processed: 443 average time/residue: 0.6012 time to fit residues: 304.1878 Evaluate side-chains 405 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 370 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 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 277 GLN Chi-restraints excluded: chain G residue 345 THR 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 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: 5.9990 chunk 194 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN B 265 GLN C 243 GLN E 265 GLN F 265 GLN G 243 GLN H 265 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.196818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.174877 restraints weight = 22078.738| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.25 r_work: 0.3931 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23384 Z= 0.178 Angle : 0.641 5.005 31640 Z= 0.350 Chirality : 0.046 0.136 3648 Planarity : 0.004 0.040 3976 Dihedral : 10.055 65.206 3738 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.75 % Allowed : 9.64 % Favored : 86.62 % 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: 0.41 (0.15), residues: 2952 helix: 1.32 (0.16), residues: 1144 sheet: -0.68 (0.25), residues: 416 loop : -0.21 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 105 TYR 0.017 0.002 TYR A 348 PHE 0.014 0.002 PHE A 401 HIS 0.003 0.001 HIS B 466 Details of bonding type rmsd covalent geometry : bond 0.00398 (23376) covalent geometry : angle 0.64107 (31640) hydrogen bonds : bond 0.05594 ( 915) hydrogen bonds : angle 4.87759 ( 2583) Misc. bond : bond 0.00063 ( 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 470 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 381 time to evaluate : 0.808 Fit side-chains REVERT: A 1 MET cc_start: 0.5925 (mmp) cc_final: 0.5530 (mmp) REVERT: A 98 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: A 256 ASP cc_start: 0.7839 (m-30) cc_final: 0.7368 (m-30) REVERT: A 277 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.6523 (tp40) REVERT: A 420 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7061 (ptt) REVERT: B 75 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: B 98 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: B 256 ASP cc_start: 0.7737 (m-30) cc_final: 0.7239 (m-30) REVERT: B 277 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: B 335 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6660 (mp0) REVERT: C 1 MET cc_start: 0.6021 (mmp) cc_final: 0.5691 (mmp) REVERT: C 256 ASP cc_start: 0.7865 (m-30) cc_final: 0.7549 (m-30) REVERT: C 277 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.6485 (tp40) REVERT: C 455 LYS cc_start: 0.7470 (pttt) cc_final: 0.7223 (ttpp) REVERT: D 75 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: D 98 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7192 (mm-30) REVERT: D 255 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7481 (p0) REVERT: D 256 ASP cc_start: 0.7662 (m-30) cc_final: 0.7230 (m-30) REVERT: D 277 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.6267 (tm-30) REVERT: E 75 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: E 98 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: E 242 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7508 (mttp) REVERT: E 255 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7353 (p0) REVERT: E 256 ASP cc_start: 0.7766 (m-30) cc_final: 0.7246 (m-30) REVERT: E 277 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.6461 (tp40) REVERT: E 335 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6691 (mp0) REVERT: F 1 MET cc_start: 0.6020 (mmp) cc_final: 0.5536 (mmp) REVERT: F 98 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: F 255 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7324 (p0) REVERT: F 256 ASP cc_start: 0.7727 (m-30) cc_final: 0.7185 (m-30) REVERT: F 277 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.6448 (tp40) REVERT: F 335 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6693 (mm-30) REVERT: G 75 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: G 256 ASP cc_start: 0.7845 (m-30) cc_final: 0.7382 (m-30) REVERT: G 277 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.6222 (tm-30) REVERT: G 498 GLN cc_start: 0.7373 (mt0) cc_final: 0.7165 (mt0) REVERT: H 1 MET cc_start: 0.6037 (mmp) cc_final: 0.5726 (mmp) REVERT: H 98 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: H 256 ASP cc_start: 0.7787 (m-30) cc_final: 0.7366 (m-30) REVERT: H 277 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.6317 (tp40) outliers start: 89 outliers final: 31 residues processed: 450 average time/residue: 0.6266 time to fit residues: 322.0796 Evaluate side-chains 420 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 366 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 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 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: 9.9990 chunk 217 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 235 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN B 265 GLN C 243 GLN D 21 GLN E 265 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 = 0.4238 r_free = 0.4238 target = 0.197065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175320 restraints weight = 22116.293| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.24 r_work: 0.3934 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23384 Z= 0.171 Angle : 0.622 5.091 31640 Z= 0.340 Chirality : 0.045 0.135 3648 Planarity : 0.004 0.045 3976 Dihedral : 10.103 62.911 3738 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.62 % Allowed : 10.69 % 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: 0.34 (0.15), residues: 2952 helix: 1.29 (0.16), residues: 1144 sheet: -0.69 (0.26), residues: 416 loop : -0.30 (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 H 348 PHE 0.014 0.002 PHE A 401 HIS 0.002 0.001 HIS H 92 Details of bonding type rmsd covalent geometry : bond 0.00383 (23376) covalent geometry : angle 0.62222 (31640) hydrogen bonds : bond 0.05285 ( 915) hydrogen bonds : angle 4.77561 ( 2583) Misc. bond : bond 0.00045 ( 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 453 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 367 time to evaluate : 0.869 Fit side-chains REVERT: A 1 MET cc_start: 0.5928 (mmp) cc_final: 0.5458 (mmp) REVERT: A 98 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7136 (mm-30) REVERT: A 256 ASP cc_start: 0.7815 (m-30) cc_final: 0.7349 (m-30) REVERT: A 277 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.6328 (tp40) REVERT: A 420 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7055 (ptt) REVERT: B 75 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: B 98 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: B 256 ASP cc_start: 0.7715 (m-30) cc_final: 0.7233 (m-30) REVERT: B 277 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6182 (tm-30) REVERT: B 420 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7180 (ptt) REVERT: C 1 MET cc_start: 0.6042 (mmp) cc_final: 0.5705 (mmp) REVERT: C 98 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: C 256 ASP cc_start: 0.7866 (m-30) cc_final: 0.7536 (m-30) REVERT: C 277 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.6461 (tp40) REVERT: C 455 LYS cc_start: 0.7519 (pttt) cc_final: 0.7250 (ttpp) REVERT: D 75 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: D 98 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: D 255 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7445 (p0) REVERT: D 256 ASP cc_start: 0.7696 (m-30) cc_final: 0.7259 (m-30) REVERT: D 277 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.6195 (tm-30) REVERT: E 98 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7144 (mm-30) REVERT: E 242 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7482 (mttp) REVERT: E 255 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7359 (p0) REVERT: E 256 ASP cc_start: 0.7775 (m-30) cc_final: 0.7278 (m-30) REVERT: E 277 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.6321 (tp40) REVERT: F 1 MET cc_start: 0.6021 (mmp) cc_final: 0.5511 (mmp) REVERT: F 98 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: F 255 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7374 (p0) REVERT: F 256 ASP cc_start: 0.7715 (m-30) cc_final: 0.7225 (m-30) REVERT: F 277 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.6411 (tp40) REVERT: F 335 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6662 (mm-30) REVERT: G 75 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: G 98 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: G 242 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7486 (mptp) REVERT: G 256 ASP cc_start: 0.7826 (m-30) cc_final: 0.7413 (m-30) REVERT: G 277 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.6161 (tm-30) REVERT: H 1 MET cc_start: 0.5985 (mmp) cc_final: 0.5669 (mmp) REVERT: H 98 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: H 256 ASP cc_start: 0.7782 (m-30) cc_final: 0.7363 (m-30) REVERT: H 277 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.6299 (tp40) outliers start: 86 outliers final: 33 residues processed: 432 average time/residue: 0.6234 time to fit residues: 306.5318 Evaluate side-chains 417 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 359 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 206 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 255 optimal weight: 1.9990 chunk 226 optimal weight: 0.3980 chunk 183 optimal weight: 0.7980 chunk 275 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 282 optimal weight: 0.5980 chunk 290 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN B 265 GLN C 243 GLN E 265 GLN F 265 GLN G 243 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.201747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.180417 restraints weight = 22074.665| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.23 r_work: 0.3992 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23384 Z= 0.099 Angle : 0.501 4.914 31640 Z= 0.274 Chirality : 0.040 0.127 3648 Planarity : 0.004 0.044 3976 Dihedral : 9.630 63.954 3738 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.42 % Allowed : 10.14 % 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: 0.72 (0.16), residues: 2952 helix: 1.69 (0.16), residues: 1144 sheet: -0.62 (0.26), residues: 416 loop : -0.11 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 C 92 Details of bonding type rmsd covalent geometry : bond 0.00206 (23376) covalent geometry : angle 0.50056 (31640) hydrogen bonds : bond 0.03618 ( 915) hydrogen bonds : angle 4.38355 ( 2583) Misc. bond : bond 0.00011 ( 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 499 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 394 time to evaluate : 0.724 Fit side-chains REVERT: A 1 MET cc_start: 0.5910 (mmp) cc_final: 0.5406 (mmp) REVERT: A 98 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: A 256 ASP cc_start: 0.7811 (m-30) cc_final: 0.7353 (m-30) REVERT: A 420 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.7071 (ptt) REVERT: B 75 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: B 98 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: B 256 ASP cc_start: 0.7658 (m-30) cc_final: 0.7156 (m-30) REVERT: B 277 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.5733 (tm-30) REVERT: C 1 MET cc_start: 0.6103 (mmp) cc_final: 0.5768 (mmp) REVERT: C 256 ASP cc_start: 0.7794 (m-30) cc_final: 0.7572 (m-30) REVERT: D 75 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: D 98 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7020 (mm-30) REVERT: D 255 ASP cc_start: 0.7686 (p0) cc_final: 0.7424 (p0) REVERT: D 256 ASP cc_start: 0.7661 (m-30) cc_final: 0.7222 (m-30) REVERT: D 277 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.5838 (tm-30) REVERT: E 75 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: E 98 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: E 255 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7376 (p0) REVERT: E 256 ASP cc_start: 0.7735 (m-30) cc_final: 0.7229 (m-30) REVERT: F 1 MET cc_start: 0.6012 (mmp) cc_final: 0.5491 (mmp) REVERT: F 98 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7091 (mm-30) REVERT: F 255 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7468 (p0) REVERT: F 256 ASP cc_start: 0.7698 (m-30) cc_final: 0.7182 (m-30) REVERT: F 335 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6422 (mp0) REVERT: G 75 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: G 242 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7494 (mptp) REVERT: G 256 ASP cc_start: 0.7812 (m-30) cc_final: 0.7437 (m-30) REVERT: G 277 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.5754 (tm-30) REVERT: H 1 MET cc_start: 0.5995 (mmp) cc_final: 0.5692 (mmp) REVERT: H 98 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: H 256 ASP cc_start: 0.7749 (m-30) cc_final: 0.7355 (m-30) REVERT: H 420 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7005 (ptt) outliers start: 105 outliers final: 37 residues processed: 474 average time/residue: 0.5428 time to fit residues: 297.1246 Evaluate side-chains 418 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 364 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 C residue 370 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 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 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 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 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 406 ILE Chi-restraints excluded: chain H residue 420 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 66 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 29 optimal weight: 0.4980 chunk 249 optimal weight: 0.1980 chunk 234 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 184 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4270 r_free = 0.4270 target = 0.200561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.178993 restraints weight = 22063.390| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.24 r_work: 0.3977 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23384 Z= 0.114 Angle : 0.524 5.109 31640 Z= 0.286 Chirality : 0.041 0.127 3648 Planarity : 0.004 0.044 3976 Dihedral : 9.710 63.501 3738 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.38 % Allowed : 10.61 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.16), residues: 2952 helix: 1.68 (0.16), residues: 1144 sheet: -0.66 (0.26), residues: 416 loop : -0.06 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 105 TYR 0.014 0.002 TYR B 348 PHE 0.013 0.001 PHE A 401 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00244 (23376) covalent geometry : angle 0.52353 (31640) hydrogen bonds : bond 0.04046 ( 915) hydrogen bonds : angle 4.38383 ( 2583) Misc. bond : bond 0.00019 ( 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 474 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 370 time to evaluate : 0.599 Fit side-chains REVERT: A 1 MET cc_start: 0.5970 (mmp) cc_final: 0.5464 (mmp) REVERT: A 98 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7122 (mm-30) REVERT: A 256 ASP cc_start: 0.7817 (m-30) cc_final: 0.7389 (m-30) REVERT: A 277 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.5440 (tm-30) REVERT: A 491 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: B 75 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: B 98 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7144 (mm-30) REVERT: B 256 ASP cc_start: 0.7675 (m-30) cc_final: 0.7170 (m-30) REVERT: B 277 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.5727 (tm-30) REVERT: B 491 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: C 1 MET cc_start: 0.6049 (mmp) cc_final: 0.5713 (mmp) REVERT: C 98 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7046 (mm-30) REVERT: C 256 ASP cc_start: 0.7815 (m-30) cc_final: 0.7566 (m-30) REVERT: C 455 LYS cc_start: 0.7468 (pttt) cc_final: 0.7157 (ttpp) REVERT: C 491 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: D 75 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: D 98 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7069 (mm-30) REVERT: D 255 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7436 (p0) REVERT: D 256 ASP cc_start: 0.7657 (m-30) cc_final: 0.7264 (m-30) REVERT: D 277 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.5798 (tm-30) REVERT: D 491 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: E 75 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: E 98 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: E 256 ASP cc_start: 0.7739 (m-30) cc_final: 0.7211 (m-30) REVERT: E 277 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.5811 (tm-30) REVERT: E 491 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: F 1 MET cc_start: 0.5974 (mmp) cc_final: 0.5457 (mmp) REVERT: F 98 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: F 255 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7467 (p0) REVERT: F 256 ASP cc_start: 0.7699 (m-30) cc_final: 0.7192 (m-30) REVERT: F 491 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: G 75 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: G 242 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7503 (mptp) REVERT: G 256 ASP cc_start: 0.7818 (m-30) cc_final: 0.7426 (m-30) REVERT: G 277 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.5769 (tm-30) REVERT: G 491 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: H 1 MET cc_start: 0.5969 (mmp) cc_final: 0.5673 (mmp) REVERT: H 98 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: H 256 ASP cc_start: 0.7757 (m-30) cc_final: 0.7381 (m-30) REVERT: H 277 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.5411 (tm-30) REVERT: H 420 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.7057 (ptt) REVERT: H 491 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7748 (tt0) outliers start: 104 outliers final: 44 residues processed: 446 average time/residue: 0.6043 time to fit residues: 308.6117 Evaluate side-chains 434 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 362 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 B residue 491 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 98 GLU 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 491 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 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 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 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 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 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 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 G residue 491 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 406 ILE Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 41 optimal weight: 4.9990 chunk 203 optimal weight: 0.5980 chunk 279 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 295 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 293 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 48 GLN G 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.201454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.179888 restraints weight = 22019.498| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.24 r_work: 0.3985 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23384 Z= 0.106 Angle : 0.508 5.253 31640 Z= 0.278 Chirality : 0.041 0.127 3648 Planarity : 0.004 0.047 3976 Dihedral : 9.655 63.551 3738 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.87 % Allowed : 11.41 % Favored : 84.72 % 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: 0.75 (0.16), residues: 2952 helix: 1.70 (0.16), residues: 1144 sheet: -0.72 (0.26), residues: 416 loop : -0.04 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 105 TYR 0.014 0.002 TYR A 12 PHE 0.013 0.001 PHE A 401 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00225 (23376) covalent geometry : angle 0.50788 (31640) hydrogen bonds : bond 0.03835 ( 915) hydrogen bonds : angle 4.32225 ( 2583) Misc. bond : bond 0.00014 ( 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 471 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 379 time to evaluate : 0.975 Fit side-chains REVERT: A 1 MET cc_start: 0.5954 (mmp) cc_final: 0.5452 (mmp) REVERT: A 98 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: A 256 ASP cc_start: 0.7801 (m-30) cc_final: 0.7347 (m-30) REVERT: A 277 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.5463 (tm-30) REVERT: A 491 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: B 75 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: B 98 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: B 256 ASP cc_start: 0.7678 (m-30) cc_final: 0.7202 (m-30) REVERT: B 277 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.5699 (tm-30) REVERT: B 491 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: C 1 MET cc_start: 0.6034 (mmp) cc_final: 0.5615 (mmp) REVERT: C 98 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: C 256 ASP cc_start: 0.7826 (m-30) cc_final: 0.7544 (m-30) REVERT: C 277 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.5539 (tm-30) REVERT: C 455 LYS cc_start: 0.7394 (pttt) cc_final: 0.7076 (ttpp) REVERT: C 491 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: D 75 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: D 98 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: D 255 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7441 (p0) REVERT: D 256 ASP cc_start: 0.7636 (m-30) cc_final: 0.7247 (m-30) REVERT: D 277 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.5713 (tm-30) REVERT: D 491 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: E 75 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: E 98 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: E 256 ASP cc_start: 0.7714 (m-30) cc_final: 0.7165 (m-30) REVERT: E 277 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.5441 (tm-30) REVERT: E 491 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: F 1 MET cc_start: 0.5911 (mmp) cc_final: 0.5399 (mmp) REVERT: F 98 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: F 255 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7502 (p0) REVERT: F 256 ASP cc_start: 0.7689 (m-30) cc_final: 0.7194 (m-30) REVERT: F 277 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.5513 (tm-30) REVERT: F 491 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: G 75 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: G 242 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7502 (mptp) REVERT: G 256 ASP cc_start: 0.7804 (m-30) cc_final: 0.7383 (m-30) REVERT: G 277 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.5723 (tm-30) REVERT: G 491 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: H 1 MET cc_start: 0.5944 (mmp) cc_final: 0.5552 (mmp) REVERT: H 98 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: H 256 ASP cc_start: 0.7743 (m-30) cc_final: 0.7388 (m-30) REVERT: H 277 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.5379 (tm-30) REVERT: H 491 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7752 (tt0) outliers start: 92 outliers final: 40 residues processed: 446 average time/residue: 0.6196 time to fit residues: 316.5101 Evaluate side-chains 436 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 367 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 B residue 406 ILE Chi-restraints excluded: chain B residue 491 GLU 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 C residue 491 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 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 F residue 491 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 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: 6.9990 chunk 123 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 478 GLN C 21 GLN D 478 GLN F 21 GLN G 478 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.201887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180394 restraints weight = 21973.767| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.23 r_work: 0.3993 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1970 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= 0.102 Angle : 0.499 4.934 31640 Z= 0.272 Chirality : 0.041 0.127 3648 Planarity : 0.003 0.050 3976 Dihedral : 9.601 63.292 3738 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.62 % Allowed : 12.71 % Favored : 83.67 % 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: 0.78 (0.16), residues: 2952 helix: 1.73 (0.16), residues: 1144 sheet: -0.76 (0.25), residues: 416 loop : 0.01 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 105 TYR 0.013 0.001 TYR D 12 PHE 0.012 0.001 PHE A 401 HIS 0.003 0.000 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00212 (23376) covalent geometry : angle 0.49925 (31640) hydrogen bonds : bond 0.03650 ( 915) hydrogen bonds : angle 4.23662 ( 2583) Misc. bond : bond 0.00012 ( 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 457 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 371 time to evaluate : 0.867 Fit side-chains REVERT: A 1 MET cc_start: 0.5943 (mmp) cc_final: 0.5451 (mmp) REVERT: A 98 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: A 256 ASP cc_start: 0.7793 (m-30) cc_final: 0.7353 (m-30) REVERT: A 277 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.5391 (tm-30) REVERT: A 483 MET cc_start: 0.8382 (tmm) cc_final: 0.7960 (tmm) REVERT: A 491 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: B 75 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: B 98 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: B 256 ASP cc_start: 0.7671 (m-30) cc_final: 0.7200 (m-30) REVERT: B 277 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.5673 (tm-30) REVERT: B 483 MET cc_start: 0.8398 (tmm) cc_final: 0.7994 (tmm) REVERT: B 491 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: C 1 MET cc_start: 0.6030 (mmp) cc_final: 0.5615 (mmp) REVERT: C 98 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7000 (mm-30) REVERT: C 256 ASP cc_start: 0.7820 (m-30) cc_final: 0.7581 (m-30) REVERT: C 277 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.5544 (tm-30) REVERT: C 455 LYS cc_start: 0.7395 (pttt) cc_final: 0.7074 (ttpp) REVERT: C 483 MET cc_start: 0.8383 (tmm) cc_final: 0.7954 (tmm) REVERT: C 491 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: D 75 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: D 255 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7460 (p0) REVERT: D 256 ASP cc_start: 0.7642 (m-30) cc_final: 0.7234 (m-30) REVERT: D 277 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.5697 (tm-30) REVERT: D 491 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: E 75 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: E 98 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: E 256 ASP cc_start: 0.7732 (m-30) cc_final: 0.7205 (m-30) REVERT: E 277 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.5378 (tm-30) REVERT: E 483 MET cc_start: 0.8384 (tmm) cc_final: 0.7962 (tmm) REVERT: E 491 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: F 1 MET cc_start: 0.5944 (mmp) cc_final: 0.5438 (mmp) REVERT: F 98 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: F 255 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7437 (p0) REVERT: F 256 ASP cc_start: 0.7702 (m-30) cc_final: 0.7205 (m-30) REVERT: F 277 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.5506 (tm-30) REVERT: F 491 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: G 75 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: G 242 LYS cc_start: 0.7687 (mtmt) cc_final: 0.7360 (mptp) REVERT: G 255 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7208 (p0) REVERT: G 256 ASP cc_start: 0.7804 (m-30) cc_final: 0.7400 (m-30) REVERT: G 277 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.5719 (tm-30) REVERT: G 491 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: H 1 MET cc_start: 0.5949 (mmp) cc_final: 0.5656 (mmp) REVERT: H 98 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: H 256 ASP cc_start: 0.7715 (m-30) cc_final: 0.7384 (m-30) REVERT: H 277 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.5356 (tm-30) REVERT: H 483 MET cc_start: 0.8408 (tmm) cc_final: 0.8001 (tmm) REVERT: H 491 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7771 (tt0) outliers start: 86 outliers final: 33 residues processed: 431 average time/residue: 0.6191 time to fit residues: 304.4899 Evaluate side-chains 431 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 369 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 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 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 491 GLU 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 C residue 491 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 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 491 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 255 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 2 optimal weight: 0.5980 chunk 141 optimal weight: 0.3980 chunk 251 optimal weight: 10.0000 chunk 241 optimal weight: 0.5980 chunk 265 optimal weight: 0.3980 chunk 138 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 478 GLN C 265 GLN D 265 GLN D 478 GLN E 296 ASN F 21 GLN F 265 GLN F 296 ASN F 478 GLN G 265 GLN G 478 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.201923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.180320 restraints weight = 22071.628| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.24 r_work: 0.3993 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1986 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= 0.103 Angle : 0.500 5.907 31640 Z= 0.272 Chirality : 0.041 0.126 3648 Planarity : 0.003 0.048 3976 Dihedral : 9.604 63.132 3738 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.49 % Allowed : 12.58 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 2952 helix: 1.73 (0.16), residues: 1144 sheet: -0.84 (0.25), residues: 416 loop : 0.01 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 105 TYR 0.014 0.001 TYR H 12 PHE 0.013 0.001 PHE A 401 HIS 0.003 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00215 (23376) covalent geometry : angle 0.49958 (31640) hydrogen bonds : bond 0.03691 ( 915) hydrogen bonds : angle 4.22784 ( 2583) Misc. bond : bond 0.00012 ( 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 451 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 368 time to evaluate : 0.644 Fit side-chains REVERT: A 1 MET cc_start: 0.5959 (mmp) cc_final: 0.5467 (mmp) REVERT: A 98 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: A 256 ASP cc_start: 0.7784 (m-30) cc_final: 0.7377 (m-30) REVERT: A 277 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.5356 (tm-30) REVERT: A 483 MET cc_start: 0.8381 (tmm) cc_final: 0.7941 (tmm) REVERT: A 491 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: B 75 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: B 98 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7049 (mm-30) REVERT: B 256 ASP cc_start: 0.7677 (m-30) cc_final: 0.7179 (m-30) REVERT: B 277 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.5717 (tm-30) REVERT: B 483 MET cc_start: 0.8396 (tmm) cc_final: 0.7982 (tmm) REVERT: B 491 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: C 1 MET cc_start: 0.6037 (mmp) cc_final: 0.5632 (mmp) REVERT: C 98 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: C 256 ASP cc_start: 0.7830 (m-30) cc_final: 0.7595 (m-30) REVERT: C 277 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.5543 (tm-30) REVERT: C 455 LYS cc_start: 0.7391 (pttt) cc_final: 0.7065 (ttpp) REVERT: C 483 MET cc_start: 0.8383 (tmm) cc_final: 0.7951 (tmm) REVERT: C 491 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: D 75 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: D 255 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7450 (p0) REVERT: D 256 ASP cc_start: 0.7643 (m-30) cc_final: 0.7252 (m-30) REVERT: D 277 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.5687 (tm-30) REVERT: D 482 MET cc_start: 0.8577 (mtp) cc_final: 0.8339 (mtm) REVERT: D 483 MET cc_start: 0.8408 (tmm) cc_final: 0.8006 (tmm) REVERT: D 491 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: E 75 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: E 98 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: E 256 ASP cc_start: 0.7733 (m-30) cc_final: 0.7207 (m-30) REVERT: E 277 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.5354 (tm-30) REVERT: E 483 MET cc_start: 0.8380 (tmm) cc_final: 0.7941 (tmm) REVERT: E 491 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: F 1 MET cc_start: 0.5944 (mmp) cc_final: 0.5440 (mmp) REVERT: F 98 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: F 255 ASP cc_start: 0.7699 (p0) cc_final: 0.7435 (p0) REVERT: F 256 ASP cc_start: 0.7693 (m-30) cc_final: 0.7214 (m-30) REVERT: F 277 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.5500 (tm-30) REVERT: F 483 MET cc_start: 0.8414 (tmm) cc_final: 0.8012 (tmm) REVERT: F 491 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: G 75 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: G 242 LYS cc_start: 0.7705 (mtmt) cc_final: 0.7371 (mptp) REVERT: G 255 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7204 (p0) REVERT: G 256 ASP cc_start: 0.7801 (m-30) cc_final: 0.7379 (m-30) REVERT: G 277 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.5701 (tm-30) REVERT: G 491 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: H 1 MET cc_start: 0.5969 (mmp) cc_final: 0.5585 (mmp) REVERT: H 98 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7094 (mm-30) REVERT: H 256 ASP cc_start: 0.7726 (m-30) cc_final: 0.7369 (m-30) REVERT: H 277 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.5335 (tm-30) REVERT: H 483 MET cc_start: 0.8409 (tmm) cc_final: 0.7986 (tmm) REVERT: H 491 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7759 (tt0) outliers start: 83 outliers final: 38 residues processed: 430 average time/residue: 0.6002 time to fit residues: 295.1100 Evaluate side-chains 437 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 371 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 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 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 491 GLU 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 C residue 491 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 98 GLU Chi-restraints excluded: chain E residue 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 277 GLN Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 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: 10.0000 chunk 94 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 478 GLN D 265 GLN D 478 GLN E 265 GLN E 296 ASN F 265 GLN F 296 ASN F 478 GLN G 21 GLN G 243 GLN G 265 GLN G 478 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.194843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172838 restraints weight = 22034.912| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.24 r_work: 0.3906 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 23384 Z= 0.289 Angle : 0.781 6.798 31640 Z= 0.425 Chirality : 0.054 0.201 3648 Planarity : 0.005 0.046 3976 Dihedral : 10.552 68.607 3736 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.20 % Allowed : 12.92 % 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: 0.04 (0.15), residues: 2952 helix: 0.94 (0.15), residues: 1144 sheet: -0.94 (0.26), residues: 416 loop : -0.32 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 105 TYR 0.020 0.003 TYR C 348 PHE 0.017 0.003 PHE E 401 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00665 (23376) covalent geometry : angle 0.78093 (31640) hydrogen bonds : bond 0.06613 ( 915) hydrogen bonds : angle 4.98590 ( 2583) Misc. bond : bond 0.00072 ( 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 448 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 372 time to evaluate : 0.575 Fit side-chains REVERT: A 1 MET cc_start: 0.5874 (mmp) cc_final: 0.5350 (mmp) REVERT: A 98 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7192 (mm-30) REVERT: A 256 ASP cc_start: 0.7795 (m-30) cc_final: 0.7424 (m-30) REVERT: A 277 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.5656 (tm-30) REVERT: A 286 MET cc_start: 0.8897 (tpp) cc_final: 0.8568 (tpp) REVERT: B 75 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: B 98 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: B 256 ASP cc_start: 0.7691 (m-30) cc_final: 0.7246 (m-30) REVERT: B 277 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.6055 (tm-30) REVERT: C 1 MET cc_start: 0.6086 (mmp) cc_final: 0.5567 (mmp) REVERT: C 98 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7223 (mm-30) REVERT: C 256 ASP cc_start: 0.7848 (m-30) cc_final: 0.7555 (m-30) REVERT: C 277 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.5673 (tm-30) REVERT: C 455 LYS cc_start: 0.7502 (pttt) cc_final: 0.7203 (ttpp) REVERT: D 98 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: D 255 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7395 (p0) REVERT: D 256 ASP cc_start: 0.7674 (m-30) cc_final: 0.7218 (m-30) REVERT: D 277 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.6067 (tm-30) REVERT: E 98 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: E 256 ASP cc_start: 0.7734 (m-30) cc_final: 0.7277 (m-30) REVERT: E 277 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.5643 (tm-30) REVERT: F 1 MET cc_start: 0.6022 (mmp) cc_final: 0.5458 (mmp) REVERT: F 98 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: F 255 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7343 (p0) REVERT: F 256 ASP cc_start: 0.7720 (m-30) cc_final: 0.7274 (m-30) REVERT: F 277 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.5597 (tm-30) REVERT: G 98 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: G 255 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7291 (p0) REVERT: G 256 ASP cc_start: 0.7861 (m-30) cc_final: 0.7449 (m-30) REVERT: G 277 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.6126 (tm-30) REVERT: H 1 MET cc_start: 0.6006 (mmp) cc_final: 0.5509 (mmp) REVERT: H 75 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8074 (mt-10) REVERT: H 98 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: H 256 ASP cc_start: 0.7825 (m-30) cc_final: 0.7394 (m-30) REVERT: H 277 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.5575 (tm-30) outliers start: 76 outliers final: 38 residues processed: 433 average time/residue: 0.6218 time to fit residues: 305.4701 Evaluate side-chains 414 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 356 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 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 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 98 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 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 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 251 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 122 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 21 GLN B 48 GLN B 265 GLN B 478 GLN C 21 GLN C 265 GLN D 21 GLN D 48 GLN D 265 GLN D 478 GLN E 48 GLN E 265 GLN F 243 GLN F 265 GLN F 478 GLN G 21 GLN G 48 GLN G 243 GLN G 265 GLN G 478 GLN H 21 GLN H 265 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.201357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.179895 restraints weight = 21970.876| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.23 r_work: 0.3989 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23384 Z= 0.103 Angle : 0.510 5.592 31640 Z= 0.278 Chirality : 0.041 0.126 3648 Planarity : 0.004 0.045 3976 Dihedral : 9.845 63.786 3736 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.61 % Allowed : 13.68 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2952 helix: 1.58 (0.16), residues: 1144 sheet: -0.92 (0.26), residues: 416 loop : -0.14 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 105 TYR 0.014 0.001 TYR A 12 PHE 0.013 0.001 PHE H 401 HIS 0.004 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00216 (23376) covalent geometry : angle 0.51000 (31640) hydrogen bonds : bond 0.03598 ( 915) hydrogen bonds : angle 4.35051 ( 2583) Misc. bond : bond 0.00028 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9639.88 seconds wall clock time: 164 minutes 27.13 seconds (9867.13 seconds total)