Starting phenix.real_space_refine on Wed Feb 4 14:37:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mub_48627/02_2026/9mub_48627.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mub_48627/02_2026/9mub_48627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mub_48627/02_2026/9mub_48627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mub_48627/02_2026/9mub_48627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mub_48627/02_2026/9mub_48627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mub_48627/02_2026/9mub_48627.map" } resolution = 2.5 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= 0.196 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 12 5.49 5 S 68 5.16 5 C 6940 2.51 5 N 1896 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s 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: 11052 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2696 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 348} Chain breaks: 2 Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2696 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 348} Chain breaks: 2 Chain: "C" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2696 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 348} Chain breaks: 2 Chain: "D" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2696 Classifications: {'peptide': 360} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 348} 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} Time building chain proxies: 2.39, per 1000 atoms: 0.22 Number of scatterers: 11052 At special positions: 0 Unit cell: (114.165, 114.165, 64.605, 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 68 16.00 P 12 15.00 O 2136 8.00 N 1896 7.00 C 6940 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 498.5 milliseconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 16 sheets defined 43.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 254 through 266 removed outlier: 4.053A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.589A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.830A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 471 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 19 through 25 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.974A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.616A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.830A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 471 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 19 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.062A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.605A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 removed outlier: 3.819A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 452 through 471 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 19 through 25 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 254 through 266 removed outlier: 4.061A pdb=" N TYR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.614A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 316 removed outlier: 3.813A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 471 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 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: 3.589A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N GLY A 302 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.512A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.976A 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: 3.948A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.685A 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 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.602A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.165A 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: 3.947A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.678A 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 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.696A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.123A 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: 3.962A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.577A 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 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.643A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N GLY D 302 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1272 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: 1.37 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2699 1.33 - 1.46: 2133 1.46 - 1.58: 6272 1.58 - 1.70: 20 1.70 - 1.83: 112 Bond restraints: 11236 Sorted by residual: bond pdb=" C5 IMP B 601 " pdb=" C6 IMP B 601 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.85e+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 1.85e+01 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=" C5 IMP A 601 " pdb=" C6 IMP A 601 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C5 IMP D 601 " pdb=" C6 IMP D 601 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 11231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 11965 2.27 - 4.54: 2825 4.54 - 6.81: 387 6.81 - 9.08: 15 9.08 - 11.35: 8 Bond angle restraints: 15200 Sorted by residual: angle pdb=" N THR B 74 " pdb=" CA THR B 74 " pdb=" C THR B 74 " ideal model delta sigma weight residual 108.02 119.37 -11.35 1.75e+00 3.27e-01 4.20e+01 angle pdb=" N THR A 74 " pdb=" CA THR A 74 " pdb=" C THR A 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 D 74 " pdb=" CA THR D 74 " pdb=" C THR D 74 " ideal model delta sigma weight residual 108.02 119.04 -11.02 1.75e+00 3.27e-01 3.96e+01 angle pdb=" N THR C 74 " pdb=" CA THR C 74 " pdb=" C THR C 74 " ideal model delta sigma weight residual 108.02 118.93 -10.91 1.75e+00 3.27e-01 3.88e+01 angle pdb=" OE1 GLN C 100 " pdb=" CD GLN C 100 " pdb=" NE2 GLN C 100 " ideal model delta sigma weight residual 122.60 116.88 5.72 1.00e+00 1.00e+00 3.27e+01 ... (remaining 15195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.72: 6239 23.72 - 47.44: 487 47.44 - 71.16: 94 71.16 - 94.88: 16 94.88 - 118.60: 4 Dihedral angle restraints: 6840 sinusoidal: 2776 harmonic: 4064 Sorted by residual: 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 -49.47 -118.60 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" C5' IMP D 601 " pdb=" O5' IMP D 601 " pdb=" P IMP D 601 " pdb=" O2P IMP D 601 " ideal model delta sinusoidal sigma weight residual -168.07 -49.66 -118.41 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" C5' IMP C 601 " pdb=" O5' IMP C 601 " pdb=" P IMP C 601 " pdb=" O2P IMP C 601 " ideal model delta sinusoidal sigma weight residual -168.07 -50.32 -117.75 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 6837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1125 0.083 - 0.166: 501 0.166 - 0.248: 109 0.248 - 0.331: 12 0.331 - 0.414: 9 Chirality restraints: 1756 Sorted by residual: chirality pdb=" CA ASP C 47 " pdb=" N ASP C 47 " pdb=" C ASP C 47 " pdb=" CB ASP C 47 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA ASP D 47 " pdb=" N ASP D 47 " pdb=" C ASP D 47 " pdb=" CB ASP D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA ASP A 47 " pdb=" N ASP A 47 " pdb=" C ASP A 47 " pdb=" CB ASP A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 1753 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 348 " 0.140 2.00e-02 2.50e+03 7.58e-02 1.15e+02 pdb=" CG TYR B 348 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 348 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR B 348 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR B 348 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR B 348 " -0.038 2.00e-02 2.50e+03 pdb=" CZ TYR B 348 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 348 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP B 601 " -0.135 2.00e-02 2.50e+03 6.76e-02 1.14e+02 pdb=" C2 IMP B 601 " 0.013 2.00e-02 2.50e+03 pdb=" C4 IMP B 601 " 0.100 2.00e-02 2.50e+03 pdb=" C5 IMP B 601 " 0.027 2.00e-02 2.50e+03 pdb=" C6 IMP B 601 " -0.069 2.00e-02 2.50e+03 pdb=" C8 IMP B 601 " 0.006 2.00e-02 2.50e+03 pdb=" N1 IMP B 601 " -0.070 2.00e-02 2.50e+03 pdb=" N3 IMP B 601 " 0.069 2.00e-02 2.50e+03 pdb=" N7 IMP B 601 " 0.015 2.00e-02 2.50e+03 pdb=" N9 IMP B 601 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 348 " 0.140 2.00e-02 2.50e+03 7.55e-02 1.14e+02 pdb=" CG TYR C 348 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 348 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR C 348 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR C 348 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR C 348 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR C 348 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 348 " 0.110 2.00e-02 2.50e+03 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1064 2.78 - 3.31: 10592 3.31 - 3.84: 18307 3.84 - 4.37: 24048 4.37 - 4.90: 38323 Nonbonded interactions: 92334 Sorted by model distance: nonbonded pdb=" NE2 GLN A 469 " pdb=" O2B NAD B 602 " model vdw 2.250 3.120 nonbonded pdb=" NE2 GLN C 469 " pdb=" O2B NAD D 602 " model vdw 2.266 3.120 nonbonded pdb=" NE2 GLN D 469 " pdb=" O2B NAD A 602 " model vdw 2.277 3.120 nonbonded pdb=" NE2 GLN B 469 " pdb=" O2B NAD C 602 " model vdw 2.285 3.120 nonbonded pdb=" O THR A 252 " pdb=" N6A NAD A 602 " model vdw 2.381 3.120 ... (remaining 92329 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' } 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.014 0.332 11240 Z= 0.922 Angle : 1.918 11.346 15200 Z= 1.249 Chirality : 0.094 0.414 1756 Planarity : 0.014 0.161 1908 Dihedral : 17.467 118.600 4256 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.49 % Allowed : 12.19 % Favored : 86.32 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.03 (0.21), residues: 1416 helix: 0.18 (0.20), residues: 560 sheet: -0.34 (0.37), residues: 144 loop : 0.14 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 341 TYR 0.140 0.026 TYR B 348 PHE 0.067 0.014 PHE D 24 HIS 0.009 0.003 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.01272 (11236) covalent geometry : angle 1.91796 (15200) hydrogen bonds : bond 0.18384 ( 449) hydrogen bonds : angle 6.87336 ( 1272) Misc. bond : bond 0.27160 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 0.409 Fit side-chains REVERT: A 265 GLN cc_start: 0.8048 (mt0) cc_final: 0.7825 (mm-40) REVERT: A 311 LYS cc_start: 0.8644 (tttp) cc_final: 0.8384 (tttp) REVERT: B 261 ASP cc_start: 0.7822 (m-30) cc_final: 0.7469 (m-30) REVERT: B 277 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8861 (tm-30) REVERT: B 335 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7186 (mp0) REVERT: B 494 THR cc_start: 0.8478 (m) cc_final: 0.8236 (p) REVERT: C 261 ASP cc_start: 0.7911 (m-30) cc_final: 0.7639 (m-30) REVERT: C 399 GLU cc_start: 0.6661 (pm20) cc_final: 0.6443 (pm20) REVERT: D 261 ASP cc_start: 0.7828 (m-30) cc_final: 0.7602 (m-30) REVERT: D 277 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8944 (tm-30) REVERT: D 414 MET cc_start: 0.9015 (mmm) cc_final: 0.8760 (mmm) outliers start: 17 outliers final: 4 residues processed: 242 average time/residue: 0.7337 time to fit residues: 188.2573 Evaluate side-chains 205 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 453 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 92 HIS A 94 ASN A 100 GLN A 243 GLN A 265 GLN A 285 ASN A 334 GLN A 368 GLN A 441 GLN A 478 GLN B 92 HIS B 93 HIS B 94 ASN B 100 GLN B 243 GLN B 285 ASN B 334 GLN B 368 GLN B 441 GLN B 448 GLN B 478 GLN C 92 HIS C 94 ASN C 100 GLN C 243 GLN C 265 GLN C 285 ASN C 334 GLN C 368 GLN C 441 GLN C 478 GLN D 92 HIS D 94 ASN D 100 GLN D 243 GLN D 285 ASN D 334 GLN D 368 GLN D 441 GLN D 478 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117784 restraints weight = 11635.064| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.24 r_work: 0.3126 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11240 Z= 0.120 Angle : 0.543 4.362 15200 Z= 0.301 Chirality : 0.042 0.129 1756 Planarity : 0.004 0.043 1908 Dihedral : 10.571 84.323 1802 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.89 % Allowed : 12.19 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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 (0.22), residues: 1416 helix: 1.25 (0.22), residues: 560 sheet: -0.20 (0.31), residues: 216 loop : 0.22 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 480 TYR 0.011 0.001 TYR A 294 PHE 0.009 0.001 PHE D 401 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00253 (11236) covalent geometry : angle 0.54279 (15200) hydrogen bonds : bond 0.04055 ( 449) hydrogen bonds : angle 5.13025 ( 1272) Misc. bond : bond 0.00069 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.457 Fit side-chains REVERT: A 265 GLN cc_start: 0.8046 (mt0) cc_final: 0.7743 (mp10) REVERT: A 420 MET cc_start: 0.7487 (ptt) cc_final: 0.7278 (ptt) REVERT: B 335 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: B 420 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7109 (ptt) REVERT: C 254 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: C 335 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6990 (mp0) REVERT: D 277 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: D 335 GLU cc_start: 0.7759 (tt0) cc_final: 0.7467 (tt0) REVERT: D 420 MET cc_start: 0.7369 (ptt) cc_final: 0.7144 (ptt) REVERT: D 512 ARG cc_start: 0.7462 (mtm180) cc_final: 0.7015 (mtp85) outliers start: 33 outliers final: 9 residues processed: 233 average time/residue: 0.8799 time to fit residues: 215.9044 Evaluate side-chains 209 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 453 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 243 GLN A 283 GLN A 368 GLN B 94 ASN B 243 GLN B 283 GLN B 368 GLN C 94 ASN C 243 GLN C 265 GLN C 283 GLN C 368 GLN D 94 ASN D 243 GLN D 283 GLN D 368 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113122 restraints weight = 11660.554| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.28 r_work: 0.3046 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11240 Z= 0.243 Angle : 0.684 5.866 15200 Z= 0.371 Chirality : 0.049 0.144 1756 Planarity : 0.005 0.047 1908 Dihedral : 10.478 60.544 1802 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.12 % Allowed : 11.84 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.50 (0.22), residues: 1416 helix: 1.19 (0.22), residues: 560 sheet: -0.29 (0.30), residues: 216 loop : -0.10 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 512 TYR 0.019 0.003 TYR A 348 PHE 0.015 0.002 PHE A 24 HIS 0.003 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00579 (11236) covalent geometry : angle 0.68404 (15200) hydrogen bonds : bond 0.06057 ( 449) hydrogen bonds : angle 5.14484 ( 1272) Misc. bond : bond 0.00141 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.416 Fit side-chains REVERT: A 261 ASP cc_start: 0.7869 (m-30) cc_final: 0.7575 (m-30) REVERT: A 265 GLN cc_start: 0.8184 (mt0) cc_final: 0.7951 (mt0) REVERT: A 315 ASP cc_start: 0.8236 (m-30) cc_final: 0.7935 (m-30) REVERT: B 261 ASP cc_start: 0.7905 (m-30) cc_final: 0.7640 (m-30) REVERT: B 315 ASP cc_start: 0.8274 (m-30) cc_final: 0.7972 (m-30) REVERT: B 335 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7046 (mp0) REVERT: B 420 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7277 (ptt) REVERT: C 98 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: C 265 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7964 (mt0) REVERT: C 335 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7066 (mp0) REVERT: D 335 GLU cc_start: 0.7905 (tt0) cc_final: 0.7547 (tt0) outliers start: 47 outliers final: 20 residues processed: 243 average time/residue: 0.7845 time to fit residues: 201.5428 Evaluate side-chains 221 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 311 LYS Chi-restraints excluded: chain D residue 345 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 94 ASN A 243 GLN A 283 GLN A 368 GLN B 22 GLN B 94 ASN B 243 GLN B 265 GLN B 283 GLN B 368 GLN C 22 GLN C 94 ASN C 243 GLN C 283 GLN C 368 GLN D 22 GLN D 94 ASN D 243 GLN D 265 GLN D 283 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118238 restraints weight = 11668.656| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.28 r_work: 0.3141 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11240 Z= 0.101 Angle : 0.487 4.185 15200 Z= 0.271 Chirality : 0.040 0.125 1756 Planarity : 0.004 0.045 1908 Dihedral : 9.712 62.420 1794 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.63 % Allowed : 13.68 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.79 (0.22), residues: 1416 helix: 1.43 (0.22), residues: 576 sheet: -0.24 (0.30), residues: 216 loop : 0.09 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 512 TYR 0.010 0.001 TYR A 348 PHE 0.008 0.001 PHE C 401 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00222 (11236) covalent geometry : angle 0.48686 (15200) hydrogen bonds : bond 0.03883 ( 449) hydrogen bonds : angle 4.72546 ( 1272) Misc. bond : bond 0.00068 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.432 Fit side-chains REVERT: A 261 ASP cc_start: 0.7840 (m-30) cc_final: 0.7570 (m-30) REVERT: A 315 ASP cc_start: 0.8193 (m-30) cc_final: 0.7873 (m-30) REVERT: B 315 ASP cc_start: 0.8273 (m-30) cc_final: 0.7981 (m-30) REVERT: B 335 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6942 (mp0) REVERT: C 311 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8570 (tttp) REVERT: C 335 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6981 (mp0) REVERT: D 335 GLU cc_start: 0.7887 (tt0) cc_final: 0.7537 (tt0) outliers start: 30 outliers final: 10 residues processed: 226 average time/residue: 0.8363 time to fit residues: 199.3478 Evaluate side-chains 214 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 311 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 94 ASN A 243 GLN A 265 GLN A 283 GLN A 368 GLN B 94 ASN B 243 GLN B 265 GLN B 283 GLN B 368 GLN B 448 GLN C 94 ASN C 243 GLN C 265 GLN C 283 GLN C 368 GLN D 94 ASN D 243 GLN D 265 GLN D 283 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.135921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115795 restraints weight = 11639.693| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.28 r_work: 0.3108 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11240 Z= 0.143 Angle : 0.542 4.365 15200 Z= 0.298 Chirality : 0.042 0.129 1756 Planarity : 0.004 0.046 1908 Dihedral : 9.809 61.077 1794 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.89 % Allowed : 13.51 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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 (0.22), residues: 1416 helix: 1.37 (0.22), residues: 576 sheet: -0.28 (0.30), residues: 216 loop : 0.03 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 512 TYR 0.014 0.002 TYR A 348 PHE 0.011 0.001 PHE C 24 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00330 (11236) covalent geometry : angle 0.54196 (15200) hydrogen bonds : bond 0.04678 ( 449) hydrogen bonds : angle 4.76282 ( 1272) Misc. bond : bond 0.00065 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.450 Fit side-chains REVERT: A 261 ASP cc_start: 0.7837 (m-30) cc_final: 0.7593 (m-30) REVERT: A 315 ASP cc_start: 0.8226 (m-30) cc_final: 0.7880 (m-30) REVERT: B 315 ASP cc_start: 0.8296 (m-30) cc_final: 0.7935 (m-30) REVERT: B 335 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6978 (mp0) REVERT: C 315 ASP cc_start: 0.8220 (m-30) cc_final: 0.8004 (m-30) REVERT: C 335 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6974 (mp0) REVERT: D 335 GLU cc_start: 0.7956 (tt0) cc_final: 0.7584 (tt0) outliers start: 33 outliers final: 17 residues processed: 234 average time/residue: 0.8139 time to fit residues: 201.4232 Evaluate side-chains 220 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 345 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 135 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 119 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 243 GLN A 265 GLN A 368 GLN B 94 ASN B 243 GLN C 94 ASN C 243 GLN C 368 GLN D 94 ASN D 243 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118285 restraints weight = 11726.174| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.24 r_work: 0.3154 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11240 Z= 0.099 Angle : 0.469 4.277 15200 Z= 0.260 Chirality : 0.039 0.124 1756 Planarity : 0.004 0.044 1908 Dihedral : 9.414 61.613 1794 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.19 % Allowed : 13.60 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.86 (0.22), residues: 1416 helix: 1.46 (0.22), residues: 580 sheet: -0.32 (0.30), residues: 216 loop : 0.18 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 512 TYR 0.010 0.001 TYR A 348 PHE 0.008 0.001 PHE D 401 HIS 0.003 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00219 (11236) covalent geometry : angle 0.46934 (15200) hydrogen bonds : bond 0.03705 ( 449) hydrogen bonds : angle 4.56689 ( 1272) Misc. bond : bond 0.00047 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.492 Fit side-chains REVERT: A 315 ASP cc_start: 0.8214 (m-30) cc_final: 0.7869 (m-30) REVERT: B 315 ASP cc_start: 0.8281 (m-30) cc_final: 0.7949 (m-30) REVERT: B 335 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7027 (mp0) REVERT: C 311 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8329 (tttp) REVERT: C 315 ASP cc_start: 0.8125 (m-30) cc_final: 0.7919 (m-30) REVERT: C 335 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6965 (mp0) REVERT: C 450 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7381 (ttmt) REVERT: D 102 ASN cc_start: 0.8077 (t0) cc_final: 0.7808 (t0) REVERT: D 335 GLU cc_start: 0.7897 (tt0) cc_final: 0.7546 (tt0) outliers start: 25 outliers final: 16 residues processed: 225 average time/residue: 0.8566 time to fit residues: 203.3885 Evaluate side-chains 218 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 345 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 0.0980 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 243 GLN A 265 GLN A 368 GLN B 94 ASN B 243 GLN B 283 GLN B 368 GLN C 94 ASN C 243 GLN C 283 GLN C 368 GLN D 94 ASN D 243 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116896 restraints weight = 11704.450| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.24 r_work: 0.3156 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11240 Z= 0.110 Angle : 0.484 4.169 15200 Z= 0.268 Chirality : 0.040 0.125 1756 Planarity : 0.004 0.043 1908 Dihedral : 9.422 61.335 1794 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.46 % Allowed : 13.77 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.84 (0.22), residues: 1416 helix: 1.46 (0.22), residues: 580 sheet: -0.39 (0.29), residues: 216 loop : 0.19 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 512 TYR 0.012 0.001 TYR A 348 PHE 0.009 0.001 PHE C 24 HIS 0.003 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00249 (11236) covalent geometry : angle 0.48431 (15200) hydrogen bonds : bond 0.04028 ( 449) hydrogen bonds : angle 4.57709 ( 1272) Misc. bond : bond 0.00055 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.439 Fit side-chains REVERT: A 315 ASP cc_start: 0.8233 (m-30) cc_final: 0.7885 (m-30) REVERT: B 315 ASP cc_start: 0.8291 (m-30) cc_final: 0.7942 (m-30) REVERT: B 335 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7022 (mp0) REVERT: C 335 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6984 (mp0) REVERT: C 439 VAL cc_start: 0.8164 (m) cc_final: 0.7717 (t) REVERT: C 450 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7376 (ttmt) REVERT: D 102 ASN cc_start: 0.8080 (t0) cc_final: 0.7804 (t0) REVERT: D 335 GLU cc_start: 0.7929 (tt0) cc_final: 0.7570 (tt0) outliers start: 28 outliers final: 17 residues processed: 230 average time/residue: 0.8814 time to fit residues: 213.6885 Evaluate side-chains 224 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 345 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 243 GLN A 283 GLN A 368 GLN B 94 ASN B 243 GLN B 265 GLN B 283 GLN C 94 ASN C 243 GLN C 283 GLN C 368 GLN D 94 ASN D 243 GLN D 265 GLN D 283 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113907 restraints weight = 11634.859| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.27 r_work: 0.3072 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11240 Z= 0.241 Angle : 0.659 5.453 15200 Z= 0.358 Chirality : 0.048 0.142 1756 Planarity : 0.005 0.046 1908 Dihedral : 10.044 59.736 1794 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.33 % Allowed : 13.68 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1416 helix: 1.29 (0.22), residues: 568 sheet: -0.45 (0.29), residues: 216 loop : -0.22 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 512 TYR 0.019 0.003 TYR A 348 PHE 0.014 0.002 PHE A 24 HIS 0.003 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00575 (11236) covalent geometry : angle 0.65868 (15200) hydrogen bonds : bond 0.05757 ( 449) hydrogen bonds : angle 4.92946 ( 1272) Misc. bond : bond 0.00116 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.463 Fit side-chains REVERT: A 315 ASP cc_start: 0.8246 (m-30) cc_final: 0.7922 (m-30) REVERT: B 315 ASP cc_start: 0.8300 (m-30) cc_final: 0.7934 (m-30) REVERT: B 335 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6989 (mp0) REVERT: C 311 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8401 (tttp) REVERT: C 335 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7030 (mp0) REVERT: C 439 VAL cc_start: 0.8289 (m) cc_final: 0.7856 (t) REVERT: D 75 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: D 335 GLU cc_start: 0.7971 (tt0) cc_final: 0.7566 (tt0) outliers start: 38 outliers final: 21 residues processed: 237 average time/residue: 0.7198 time to fit residues: 180.3582 Evaluate side-chains 229 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 345 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 94 ASN A 243 GLN A 368 GLN B 94 ASN B 243 GLN B 283 GLN B 368 GLN C 94 ASN C 243 GLN C 283 GLN C 368 GLN D 94 ASN D 243 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116623 restraints weight = 11605.629| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.23 r_work: 0.3132 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11240 Z= 0.118 Angle : 0.503 4.156 15200 Z= 0.279 Chirality : 0.041 0.128 1756 Planarity : 0.004 0.045 1908 Dihedral : 9.606 61.843 1794 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.11 % Allowed : 15.00 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.66 (0.22), residues: 1416 helix: 1.33 (0.22), residues: 580 sheet: -0.40 (0.29), residues: 216 loop : 0.03 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 512 TYR 0.011 0.001 TYR A 348 PHE 0.009 0.001 PHE C 24 HIS 0.003 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00266 (11236) covalent geometry : angle 0.50268 (15200) hydrogen bonds : bond 0.04132 ( 449) hydrogen bonds : angle 4.68293 ( 1272) Misc. bond : bond 0.00065 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.463 Fit side-chains REVERT: A 315 ASP cc_start: 0.8212 (m-30) cc_final: 0.7878 (m-30) REVERT: B 315 ASP cc_start: 0.8255 (m-30) cc_final: 0.7899 (m-30) REVERT: B 335 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7004 (mp0) REVERT: C 335 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6993 (mp0) REVERT: C 439 VAL cc_start: 0.8213 (m) cc_final: 0.7802 (t) REVERT: D 335 GLU cc_start: 0.7944 (tt0) cc_final: 0.7569 (tt0) outliers start: 24 outliers final: 17 residues processed: 228 average time/residue: 0.7911 time to fit residues: 190.4394 Evaluate side-chains 218 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 243 GLN A 368 GLN B 94 ASN B 243 GLN B 265 GLN B 283 GLN C 94 ASN C 243 GLN C 283 GLN C 368 GLN D 48 GLN D 94 ASN D 243 GLN D 265 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.116781 restraints weight = 11680.752| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.24 r_work: 0.3186 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11240 Z= 0.115 Angle : 0.496 4.153 15200 Z= 0.275 Chirality : 0.041 0.125 1756 Planarity : 0.004 0.044 1908 Dihedral : 9.454 61.784 1794 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.58 % Allowed : 15.79 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.71 (0.22), residues: 1416 helix: 1.36 (0.22), residues: 580 sheet: -0.45 (0.29), residues: 216 loop : 0.09 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 512 TYR 0.011 0.001 TYR A 348 PHE 0.009 0.001 PHE C 24 HIS 0.003 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00260 (11236) covalent geometry : angle 0.49564 (15200) hydrogen bonds : bond 0.04074 ( 449) hydrogen bonds : angle 4.60727 ( 1272) Misc. bond : bond 0.00058 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.441 Fit side-chains REVERT: A 315 ASP cc_start: 0.8209 (m-30) cc_final: 0.7880 (m-30) REVERT: B 315 ASP cc_start: 0.8257 (m-30) cc_final: 0.7908 (m-30) REVERT: B 335 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7003 (mp0) REVERT: C 335 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7000 (mp0) REVERT: C 439 VAL cc_start: 0.8165 (m) cc_final: 0.7762 (t) REVERT: D 335 GLU cc_start: 0.7949 (tt0) cc_final: 0.7599 (tt0) outliers start: 18 outliers final: 16 residues processed: 227 average time/residue: 0.7725 time to fit residues: 185.0385 Evaluate side-chains 220 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 0.0980 chunk 123 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 243 GLN A 283 GLN A 368 GLN B 94 ASN B 243 GLN B 265 GLN B 283 GLN C 94 ASN C 243 GLN C 283 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 243 GLN D 265 GLN D 283 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.114623 restraints weight = 11579.199| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.23 r_work: 0.3101 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11240 Z= 0.181 Angle : 0.590 4.562 15200 Z= 0.324 Chirality : 0.044 0.132 1756 Planarity : 0.005 0.045 1908 Dihedral : 9.769 60.528 1794 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.11 % Allowed : 15.70 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.29 % 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: 0.52 (0.22), residues: 1416 helix: 1.24 (0.22), residues: 580 sheet: -0.52 (0.29), residues: 216 loop : -0.05 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 512 TYR 0.015 0.002 TYR A 348 PHE 0.012 0.002 PHE A 24 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00428 (11236) covalent geometry : angle 0.58993 (15200) hydrogen bonds : bond 0.05138 ( 449) hydrogen bonds : angle 4.80002 ( 1272) Misc. bond : bond 0.00088 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4521.41 seconds wall clock time: 77 minutes 44.52 seconds (4664.52 seconds total)