Starting phenix.real_space_refine on Thu Jun 4 06:57:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mub_48627/06_2026/9mub_48627.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mub_48627/06_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_48627/06_2026/9mub_48627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mub_48627/06_2026/9mub_48627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mub_48627/06_2026/9mub_48627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mub_48627/06_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-dev-6079/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: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 3.25, per 1000 atoms: 0.29 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: 0.87 Conformation dependent library (CDL) restraints added in 637.5 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: 0.42 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: 1.94 Time building geometry restraints manager: 1.18 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=" O5' IMP A 601 " pdb=" P IMP A 601 " ideal model delta sigma weight residual 1.683 1.588 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O5' IMP B 601 " pdb=" P IMP B 601 " ideal model delta sigma weight residual 1.683 1.591 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" O5' IMP C 601 " pdb=" P IMP C 601 " ideal model delta sigma weight residual 1.683 1.591 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O5' IMP D 601 " pdb=" P IMP D 601 " ideal model delta sigma weight residual 1.683 1.591 0.092 2.00e-02 2.50e+03 2.09e+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 ... (remaining 11231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 11978 2.27 - 4.54: 2809 4.54 - 6.81: 390 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 - 17.34: 6061 17.34 - 34.67: 528 34.67 - 52.01: 227 52.01 - 69.35: 68 69.35 - 86.69: 20 Dihedral angle restraints: 6904 sinusoidal: 2840 harmonic: 4064 Sorted by residual: dihedral pdb=" C ASP C 47 " pdb=" N ASP C 47 " pdb=" CA ASP C 47 " pdb=" CB ASP C 47 " ideal model delta harmonic sigma weight residual -122.60 -134.56 11.96 0 2.50e+00 1.60e-01 2.29e+01 dihedral pdb=" C ASP A 47 " pdb=" N ASP A 47 " pdb=" CA ASP A 47 " pdb=" CB ASP A 47 " ideal model delta harmonic sigma weight residual -122.60 -134.12 11.52 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C ASP D 47 " pdb=" N ASP D 47 " pdb=" CA ASP D 47 " pdb=" CB ASP D 47 " ideal model delta harmonic sigma weight residual -122.60 -134.05 11.45 0 2.50e+00 1.60e-01 2.10e+01 ... (remaining 6901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1117 0.083 - 0.166: 510 0.166 - 0.248: 108 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=" C1' IMP B 601 " -0.169 2.00e-02 2.50e+03 7.35e-02 1.48e+02 pdb=" C2 IMP B 601 " 0.017 2.00e-02 2.50e+03 pdb=" C4 IMP B 601 " 0.101 2.00e-02 2.50e+03 pdb=" C5 IMP B 601 " 0.052 2.00e-02 2.50e+03 pdb=" C6 IMP B 601 " -0.028 2.00e-02 2.50e+03 pdb=" C8 IMP B 601 " 0.017 2.00e-02 2.50e+03 pdb=" N1 IMP B 601 " -0.042 2.00e-02 2.50e+03 pdb=" N3 IMP B 601 " 0.058 2.00e-02 2.50e+03 pdb=" N7 IMP B 601 " 0.047 2.00e-02 2.50e+03 pdb=" N9 IMP B 601 " 0.036 2.00e-02 2.50e+03 pdb=" O6 IMP B 601 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP A 601 " 0.160 2.00e-02 2.50e+03 7.13e-02 1.40e+02 pdb=" C2 IMP A 601 " -0.005 2.00e-02 2.50e+03 pdb=" C4 IMP A 601 " -0.104 2.00e-02 2.50e+03 pdb=" C5 IMP A 601 " -0.058 2.00e-02 2.50e+03 pdb=" C6 IMP A 601 " 0.023 2.00e-02 2.50e+03 pdb=" C8 IMP A 601 " -0.005 2.00e-02 2.50e+03 pdb=" N1 IMP A 601 " 0.044 2.00e-02 2.50e+03 pdb=" N3 IMP A 601 " -0.059 2.00e-02 2.50e+03 pdb=" N7 IMP A 601 " -0.042 2.00e-02 2.50e+03 pdb=" N9 IMP A 601 " -0.038 2.00e-02 2.50e+03 pdb=" O6 IMP A 601 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP D 601 " 0.159 2.00e-02 2.50e+03 7.03e-02 1.36e+02 pdb=" C2 IMP D 601 " -0.002 2.00e-02 2.50e+03 pdb=" C4 IMP D 601 " -0.106 2.00e-02 2.50e+03 pdb=" C5 IMP D 601 " -0.054 2.00e-02 2.50e+03 pdb=" C6 IMP D 601 " 0.023 2.00e-02 2.50e+03 pdb=" C8 IMP D 601 " -0.005 2.00e-02 2.50e+03 pdb=" N1 IMP D 601 " 0.047 2.00e-02 2.50e+03 pdb=" N3 IMP D 601 " -0.061 2.00e-02 2.50e+03 pdb=" N7 IMP D 601 " -0.035 2.00e-02 2.50e+03 pdb=" N9 IMP D 601 " -0.041 2.00e-02 2.50e+03 pdb=" O6 IMP D 601 " 0.075 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: 2.580 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.670 Find NCS groups from input model: 0.210 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:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- 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 : 1.921 11.346 15200 Z= 1.247 Chirality : 0.095 0.414 1756 Planarity : 0.014 0.161 1908 Dihedral : 17.069 86.686 4320 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/Z covalent geometry : bond 0.01276 / 0.77 (11236) covalent geometry : angle 1.92092 / 1.25 (15200) hydrogen bonds : bond 0.18384 / 12.45 ( 449) hydrogen bonds : angle 6.87336 / 4.78 ( 1272) Misc. bond : bond 0.27160 / 13.54 ( 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 : 0.399 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: 0.7703 time to fit residues: 197.5638 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 : 0.435 ------------------------------------------------------------------------------- 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: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.138002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118114 restraints weight = 11615.753| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.23 r_work: 0.3127 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1813 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= 0.117 Angle : 0.538 4.459 15200 Z= 0.298 Chirality : 0.042 0.130 1756 Planarity : 0.004 0.042 1908 Dihedral : 10.246 56.761 1866 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 0.74 (0.22), residues: 1416 helix: 1.25 (0.22), residues: 560 sheet: -0.20 (0.31), residues: 216 loop : 0.21 (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 0.008 0.001 PHE D 401 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (11236) covalent geometry : angle 0.53773 / 0.30 (15200) hydrogen bonds : bond 0.04079 / 2.75 ( 449) hydrogen bonds : angle 5.14172 / 3.61 ( 1272) Misc. bond : bond 0.00039 / 0.02 ( 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 244 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.432 Fit side-chains REVERT: A 265 GLN cc_start: 0.8050 (mt0) cc_final: 0.7745 (mp10) REVERT: A 355 ARG cc_start: 0.8373 (ptm-80) cc_final: 0.8173 (ptt90) REVERT: B 335 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: B 420 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7120 (ptt) REVERT: C 335 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6986 (mp0) REVERT: D 277 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8680 (tm-30) REVERT: D 335 GLU cc_start: 0.7763 (tt0) cc_final: 0.7471 (tt0) REVERT: D 420 MET cc_start: 0.7360 (ptt) cc_final: 0.7137 (ptt) outliers start: 33 outliers final: 8 residues processed: 230 average time/residue: 0.8789 time to fit residues: 212.6897 Evaluate side-chains 206 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 27 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.114942 restraints weight = 11653.600| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.29 r_work: 0.3082 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11240 Z= 0.176 Angle : 0.595 5.285 15200 Z= 0.327 Chirality : 0.045 0.133 1756 Planarity : 0.005 0.046 1908 Dihedral : 10.331 60.217 1866 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.86 % Allowed : 11.67 % Favored : 84.47 % 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: 1.35 (0.22), residues: 560 sheet: -0.29 (0.30), residues: 216 loop : 0.00 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 512 TYR 0.017 0.002 TYR C 348 PHE 0.013 0.002 PHE A 24 HIS 0.002 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (11236) covalent geometry : angle 0.59480 / 0.33 (15200) hydrogen bonds : bond 0.05382 / 3.59 ( 449) hydrogen bonds : angle 4.99533 / 3.50 ( 1272) Misc. bond : bond 0.00114 / 0.06 ( 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 254 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.382 Fit side-chains REVERT: A 261 ASP cc_start: 0.7835 (m-30) cc_final: 0.7522 (m-30) REVERT: A 265 GLN cc_start: 0.8150 (mt0) cc_final: 0.7922 (mt0) REVERT: A 315 ASP cc_start: 0.8224 (m-30) cc_final: 0.7941 (m-30) REVERT: B 261 ASP cc_start: 0.7917 (m-30) cc_final: 0.7681 (m-30) REVERT: B 315 ASP cc_start: 0.8260 (m-30) cc_final: 0.7978 (m-30) REVERT: B 335 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7000 (mp0) REVERT: C 98 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: C 335 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6985 (mp0) REVERT: D 335 GLU cc_start: 0.7937 (tt0) cc_final: 0.7592 (tt0) outliers start: 44 outliers final: 18 residues processed: 240 average time/residue: 0.8311 time to fit residues: 210.6274 Evaluate side-chains 215 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain D residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 368 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.138229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.118469 restraints weight = 11653.611| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.24 r_work: 0.3123 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11240 Z= 0.101 Angle : 0.471 4.168 15200 Z= 0.262 Chirality : 0.040 0.125 1756 Planarity : 0.004 0.045 1908 Dihedral : 9.612 59.911 1860 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.72 % Allowed : 13.33 % Favored : 83.95 % 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: 0.80 (0.22), residues: 1416 helix: 1.44 (0.22), residues: 576 sheet: -0.34 (0.30), residues: 216 loop : 0.12 (0.25), residues: 624 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 0.007 0.001 PHE B 401 HIS 0.003 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11236) covalent geometry : angle 0.47108 / 0.26 (15200) hydrogen bonds : bond 0.03790 / 2.55 ( 449) hydrogen bonds : angle 4.62979 / 3.25 ( 1272) Misc. bond : bond 0.00054 / 0.03 ( 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 235 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.421 Fit side-chains REVERT: A 261 ASP cc_start: 0.7850 (m-30) cc_final: 0.7566 (m-30) REVERT: A 265 GLN cc_start: 0.8051 (mt0) cc_final: 0.7846 (mm110) REVERT: A 315 ASP cc_start: 0.8183 (m-30) cc_final: 0.7875 (m-30) REVERT: B 315 ASP cc_start: 0.8230 (m-30) cc_final: 0.7962 (m-30) REVERT: B 335 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6959 (mp0) REVERT: C 335 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6917 (mp0) REVERT: D 335 GLU cc_start: 0.7882 (tt0) cc_final: 0.7532 (tt0) outliers start: 31 outliers final: 14 residues processed: 225 average time/residue: 0.8652 time to fit residues: 205.1764 Evaluate side-chains 215 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 277 GLN Chi-restraints excluded: chain B residue 297 LEU 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 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 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: 4.9990 chunk 16 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 B 368 GLN C 94 ASN 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 = 0.3458 r_free = 0.3458 target = 0.135075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.114950 restraints weight = 11550.423| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.27 r_work: 0.3064 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11240 Z= 0.186 Angle : 0.587 4.603 15200 Z= 0.321 Chirality : 0.044 0.131 1756 Planarity : 0.005 0.047 1908 Dihedral : 9.966 58.734 1858 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.33 % Allowed : 12.89 % 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: 0.70 (0.22), residues: 1416 helix: 1.47 (0.22), residues: 560 sheet: -0.34 (0.29), residues: 216 loop : -0.05 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 512 TYR 0.016 0.002 TYR C 348 PHE 0.012 0.002 PHE C 24 HIS 0.002 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (11236) covalent geometry : angle 0.58709 / 0.32 (15200) hydrogen bonds : bond 0.05244 / 3.50 ( 449) hydrogen bonds : angle 4.83061 / 3.38 ( 1272) Misc. bond : bond 0.00095 / 0.05 ( 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 248 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.431 Fit side-chains REVERT: A 261 ASP cc_start: 0.7806 (m-30) cc_final: 0.7544 (m-30) REVERT: A 315 ASP cc_start: 0.8247 (m-30) cc_final: 0.7899 (m-30) REVERT: B 315 ASP cc_start: 0.8294 (m-30) cc_final: 0.7936 (m-30) REVERT: B 335 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7000 (mp0) REVERT: C 315 ASP cc_start: 0.8206 (m-30) cc_final: 0.7990 (m-30) REVERT: C 335 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7003 (mp0) REVERT: D 335 GLU cc_start: 0.7969 (tt0) cc_final: 0.7583 (tt0) outliers start: 38 outliers final: 21 residues processed: 240 average time/residue: 0.7745 time to fit residues: 196.6665 Evaluate side-chains 227 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 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 345 THR Chi-restraints excluded: chain C residue 63 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 Chi-restraints excluded: chain D residue 487 GLU 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: 5.9990 chunk 78 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 283 GLN A 368 GLN B 94 ASN B 243 GLN B 265 GLN B 283 GLN B 368 GLN C 94 ASN C 283 GLN C 368 GLN D 94 ASN D 243 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 = 0.3467 r_free = 0.3467 target = 0.135931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116313 restraints weight = 11665.483| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.23 r_work: 0.3109 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11240 Z= 0.122 Angle : 0.500 4.191 15200 Z= 0.276 Chirality : 0.041 0.125 1756 Planarity : 0.004 0.046 1908 Dihedral : 9.707 59.897 1858 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.16 % Allowed : 13.77 % Favored : 83.07 % 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: 1.44 (0.22), residues: 576 sheet: -0.39 (0.29), residues: 216 loop : -0.01 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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/Z covalent geometry : bond 0.00278 / 0.12 (11236) covalent geometry : angle 0.50027 / 0.28 (15200) hydrogen bonds : bond 0.04228 / 2.84 ( 449) hydrogen bonds : angle 4.65260 / 3.26 ( 1272) Misc. bond : bond 0.00060 / 0.03 ( 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 240 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.418 Fit side-chains REVERT: A 261 ASP cc_start: 0.7837 (m-30) cc_final: 0.7588 (m-30) REVERT: A 265 GLN cc_start: 0.8088 (mt0) cc_final: 0.7811 (mm110) REVERT: A 315 ASP cc_start: 0.8225 (m-30) cc_final: 0.7880 (m-30) REVERT: B 315 ASP cc_start: 0.8284 (m-30) cc_final: 0.7929 (m-30) REVERT: B 335 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7040 (mp0) REVERT: C 315 ASP cc_start: 0.8132 (m-30) cc_final: 0.7915 (m-30) REVERT: C 335 GLU cc_start: 0.7526 (mt-10) cc_final: 0.6994 (mp0) REVERT: C 439 VAL cc_start: 0.8187 (m) cc_final: 0.7739 (t) REVERT: C 450 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7382 (ttmt) REVERT: D 335 GLU cc_start: 0.7920 (tt0) cc_final: 0.7545 (tt0) outliers start: 36 outliers final: 19 residues processed: 234 average time/residue: 0.8090 time to fit residues: 200.0357 Evaluate side-chains 226 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR 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 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 31 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 31 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 104 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 B 368 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 D 283 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.114403 restraints weight = 11602.910| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.23 r_work: 0.3091 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11240 Z= 0.172 Angle : 0.567 4.455 15200 Z= 0.310 Chirality : 0.043 0.129 1756 Planarity : 0.004 0.047 1908 Dihedral : 9.876 58.381 1858 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.16 % Allowed : 14.47 % Favored : 82.37 % 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: 1.48 (0.22), residues: 560 sheet: -0.41 (0.29), residues: 216 loop : -0.09 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 512 TYR 0.015 0.002 TYR A 348 PHE 0.012 0.002 PHE C 24 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (11236) covalent geometry : angle 0.56672 / 0.31 (15200) hydrogen bonds : bond 0.04996 / 3.35 ( 449) hydrogen bonds : angle 4.77422 / 3.35 ( 1272) Misc. bond : bond 0.00079 / 0.04 ( 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 240 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.431 Fit side-chains REVERT: A 261 ASP cc_start: 0.7844 (m-30) cc_final: 0.7608 (m-30) REVERT: A 315 ASP cc_start: 0.8223 (m-30) cc_final: 0.7879 (m-30) REVERT: B 315 ASP cc_start: 0.8260 (m-30) cc_final: 0.7898 (m-30) REVERT: B 335 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6998 (mp0) REVERT: C 335 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7004 (mp0) REVERT: C 439 VAL cc_start: 0.8254 (m) cc_final: 0.7832 (t) REVERT: D 335 GLU cc_start: 0.7978 (tt0) cc_final: 0.7578 (tt0) outliers start: 36 outliers final: 20 residues processed: 235 average time/residue: 0.8171 time to fit residues: 202.9262 Evaluate side-chains 223 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 THR 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 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 63 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 31 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 4.9990 chunk 107 optimal weight: 0.0030 chunk 78 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 0.0570 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 0.4308 ------------------------------------------------------------------------------- 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 368 GLN B 94 ASN B 243 GLN B 368 GLN C 94 ASN C 243 GLN C 368 GLN D 48 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 = 0.3503 r_free = 0.3503 target = 0.138852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119081 restraints weight = 11640.741| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.27 r_work: 0.3149 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2362 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= 0.093 Angle : 0.455 4.100 15200 Z= 0.252 Chirality : 0.039 0.124 1756 Planarity : 0.004 0.045 1908 Dihedral : 9.402 59.922 1858 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.19 % Allowed : 15.18 % 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: 0.80 (0.22), residues: 1416 helix: 1.48 (0.22), residues: 580 sheet: -0.41 (0.29), residues: 216 loop : 0.10 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 512 TYR 0.009 0.001 TYR A 348 PHE 0.008 0.001 PHE D 401 HIS 0.003 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (11236) covalent geometry : angle 0.45489 / 0.25 (15200) hydrogen bonds : bond 0.03617 / 2.44 ( 449) hydrogen bonds : angle 4.52850 / 3.18 ( 1272) Misc. bond : bond 0.00046 / 0.02 ( 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 231 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.439 Fit side-chains REVERT: A 265 GLN cc_start: 0.8028 (mt0) cc_final: 0.7780 (mm110) REVERT: A 315 ASP cc_start: 0.8222 (m-30) cc_final: 0.7872 (m-30) REVERT: B 315 ASP cc_start: 0.8274 (m-30) cc_final: 0.7914 (m-30) REVERT: B 335 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7018 (mp0) REVERT: C 335 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6974 (mp0) REVERT: C 439 VAL cc_start: 0.8096 (m) cc_final: 0.7687 (t) REVERT: C 450 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7372 (ttmt) REVERT: D 102 ASN cc_start: 0.8069 (t0) cc_final: 0.7795 (t0) REVERT: D 265 GLN cc_start: 0.7968 (mt0) cc_final: 0.7762 (mm110) REVERT: D 335 GLU cc_start: 0.7932 (tt0) cc_final: 0.7567 (tt0) outliers start: 25 outliers final: 12 residues processed: 229 average time/residue: 0.8552 time to fit residues: 206.3265 Evaluate side-chains 221 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 277 GLN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 67 SER 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 345 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 141 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 93 optimal weight: 0.0030 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 124 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.9530 ------------------------------------------------------------------------------- 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 368 GLN B 94 ASN B 265 GLN B 283 GLN B 368 GLN C 94 ASN C 283 GLN C 368 GLN D 94 ASN D 243 GLN D 283 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.135047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.115099 restraints weight = 11626.599| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.25 r_work: 0.3125 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2289 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= 0.131 Angle : 0.509 4.212 15200 Z= 0.281 Chirality : 0.041 0.127 1756 Planarity : 0.004 0.046 1908 Dihedral : 9.577 59.237 1858 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.02 % Allowed : 15.53 % Favored : 82.46 % 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: 0.69 (0.22), residues: 1416 helix: 1.38 (0.22), residues: 580 sheet: -0.46 (0.29), residues: 216 loop : 0.05 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 512 TYR 0.013 0.001 TYR A 348 PHE 0.010 0.001 PHE C 24 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (11236) covalent geometry : angle 0.50877 / 0.28 (15200) hydrogen bonds : bond 0.04416 / 2.95 ( 449) hydrogen bonds : angle 4.63867 / 3.25 ( 1272) Misc. bond : bond 0.00058 / 0.03 ( 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 232 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.520 Fit side-chains REVERT: A 265 GLN cc_start: 0.8108 (mt0) cc_final: 0.7901 (mt0) REVERT: A 315 ASP cc_start: 0.8224 (m-30) cc_final: 0.7893 (m-30) REVERT: B 315 ASP cc_start: 0.8262 (m-30) cc_final: 0.7910 (m-30) REVERT: B 335 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7030 (mp0) REVERT: C 335 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6980 (mp0) REVERT: C 439 VAL cc_start: 0.8177 (m) cc_final: 0.7773 (t) REVERT: C 450 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7375 (ttmt) REVERT: D 335 GLU cc_start: 0.7894 (tt0) cc_final: 0.7491 (tt0) outliers start: 23 outliers final: 15 residues processed: 230 average time/residue: 0.8645 time to fit residues: 209.6219 Evaluate side-chains 223 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 137 optimal weight: 0.0050 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 368 GLN C 94 ASN C 368 GLN D 94 ASN D 243 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118195 restraints weight = 11636.487| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.24 r_work: 0.3127 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2388 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= 0.101 Angle : 0.463 4.159 15200 Z= 0.257 Chirality : 0.040 0.124 1756 Planarity : 0.004 0.045 1908 Dihedral : 9.331 59.222 1858 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 16.14 % Favored : 82.37 % 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: 1.45 (0.22), residues: 580 sheet: -0.43 (0.29), residues: 216 loop : 0.14 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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/Z covalent geometry : bond 0.00226 / 0.10 (11236) covalent geometry : angle 0.46272 / 0.26 (15200) hydrogen bonds : bond 0.03786 / 2.54 ( 449) hydrogen bonds : angle 4.53753 / 3.18 ( 1272) Misc. bond : bond 0.00043 / 0.02 ( 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 223 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.418 Fit side-chains REVERT: A 265 GLN cc_start: 0.8042 (mt0) cc_final: 0.7752 (mm110) REVERT: A 315 ASP cc_start: 0.8212 (m-30) cc_final: 0.7860 (m-30) REVERT: B 98 GLU cc_start: 0.7954 (mp0) cc_final: 0.7558 (mp0) REVERT: B 315 ASP cc_start: 0.8258 (m-30) cc_final: 0.7883 (m-30) REVERT: B 335 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6988 (mp0) REVERT: C 335 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6936 (mp0) REVERT: C 439 VAL cc_start: 0.8061 (m) cc_final: 0.7655 (t) REVERT: D 102 ASN cc_start: 0.8048 (t0) cc_final: 0.7765 (t0) REVERT: D 265 GLN cc_start: 0.7976 (mt0) cc_final: 0.7743 (mm110) REVERT: D 335 GLU cc_start: 0.7896 (tt0) cc_final: 0.7526 (tt0) outliers start: 17 outliers final: 16 residues processed: 222 average time/residue: 0.8612 time to fit residues: 201.3991 Evaluate side-chains 222 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 123 optimal weight: 0.0050 chunk 47 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 283 GLN A 368 GLN B 94 ASN B 243 GLN B 265 GLN B 283 GLN B 368 GLN C 94 ASN C 283 GLN C 368 GLN D 94 ASN D 243 GLN D 283 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.114359 restraints weight = 11583.257| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.24 r_work: 0.3109 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11240 Z= 0.162 Angle : 0.548 4.265 15200 Z= 0.301 Chirality : 0.043 0.130 1756 Planarity : 0.004 0.046 1908 Dihedral : 9.677 59.436 1858 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.93 % Allowed : 16.23 % Favored : 81.84 % 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: 0.58 (0.22), residues: 1416 helix: 1.39 (0.22), residues: 572 sheet: -0.49 (0.29), residues: 216 loop : -0.13 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 512 TYR 0.014 0.002 TYR A 348 PHE 0.011 0.002 PHE B 24 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (11236) covalent geometry : angle 0.54829 / 0.30 (15200) hydrogen bonds : bond 0.04850 / 3.24 ( 449) hydrogen bonds : angle 4.71903 / 3.30 ( 1272) Misc. bond : bond 0.00075 / 0.04 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4795.91 seconds wall clock time: 82 minutes 24.76 seconds (4944.76 seconds total)