Starting phenix.real_space_refine on Wed Feb 4 22:07:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgm_53138/02_2026/9qgm_53138.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgm_53138/02_2026/9qgm_53138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qgm_53138/02_2026/9qgm_53138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgm_53138/02_2026/9qgm_53138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qgm_53138/02_2026/9qgm_53138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgm_53138/02_2026/9qgm_53138.map" } resolution = 2.82 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= 0.003 sd= 0.059 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 8178 2.51 5 N 2259 2.21 5 O 2487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 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: 12963 Number of models: 1 Model: "" Number of chains: 6 Chain: "8A" Number of atoms: 4097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4097 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 26, 'TRANS': 500} Chain breaks: 1 Chain: "8B" Number of atoms: 4097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4097 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 26, 'TRANS': 500} Chain breaks: 1 Chain: "8C" Number of atoms: 4097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4097 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 26, 'TRANS': 500} Chain breaks: 1 Chain: "6A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 224 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "6B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 224 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "6C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 224 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Time building chain proxies: 3.21, per 1000 atoms: 0.25 Number of scatterers: 12963 At special positions: 0 Unit cell: (94.8, 94.8, 148.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 2487 8.00 N 2259 7.00 C 8178 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=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 623.6 milliseconds 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 16 sheets defined 19.5% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain '8A' and resid 50 through 60 Processing helix chain '8A' and resid 101 through 107 Processing helix chain '8A' and resid 119 through 131 removed outlier: 3.502A pdb=" N ALA8A 130 " --> pdb=" O LEU8A 126 " (cutoff:3.500A) Processing helix chain '8A' and resid 139 through 143 Processing helix chain '8A' and resid 155 through 167 Processing helix chain '8A' and resid 183 through 189 removed outlier: 3.515A pdb=" N ASN8A 187 " --> pdb=" O LYS8A 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN8A 188 " --> pdb=" O ALA8A 185 " (cutoff:3.500A) Processing helix chain '8A' and resid 249 through 254 removed outlier: 6.141A pdb=" N ASP8A 252 " --> pdb=" O LEU8A 249 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE8A 254 " --> pdb=" O VAL8A 251 " (cutoff:3.500A) Processing helix chain '8A' and resid 271 through 288 Processing helix chain '8A' and resid 422 through 424 No H-bonds generated for 'chain '8A' and resid 422 through 424' Processing helix chain '8B' and resid 50 through 60 Processing helix chain '8B' and resid 101 through 107 Processing helix chain '8B' and resid 119 through 131 removed outlier: 3.517A pdb=" N ALA8B 130 " --> pdb=" O LEU8B 126 " (cutoff:3.500A) Processing helix chain '8B' and resid 139 through 143 Processing helix chain '8B' and resid 155 through 167 Processing helix chain '8B' and resid 183 through 189 removed outlier: 3.607A pdb=" N GLN8B 188 " --> pdb=" O ALA8B 185 " (cutoff:3.500A) Processing helix chain '8B' and resid 249 through 254 removed outlier: 6.111A pdb=" N ASP8B 252 " --> pdb=" O LEU8B 249 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE8B 254 " --> pdb=" O VAL8B 251 " (cutoff:3.500A) Processing helix chain '8B' and resid 271 through 288 Processing helix chain '8B' and resid 422 through 424 No H-bonds generated for 'chain '8B' and resid 422 through 424' Processing helix chain '8C' and resid 50 through 59 Processing helix chain '8C' and resid 101 through 107 Processing helix chain '8C' and resid 119 through 131 removed outlier: 3.508A pdb=" N ALA8C 130 " --> pdb=" O LEU8C 126 " (cutoff:3.500A) Processing helix chain '8C' and resid 139 through 143 Processing helix chain '8C' and resid 155 through 167 Processing helix chain '8C' and resid 183 through 189 removed outlier: 3.622A pdb=" N GLN8C 188 " --> pdb=" O ALA8C 185 " (cutoff:3.500A) Processing helix chain '8C' and resid 249 through 254 removed outlier: 6.145A pdb=" N ASP8C 252 " --> pdb=" O LEU8C 249 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE8C 254 " --> pdb=" O VAL8C 251 " (cutoff:3.500A) Processing helix chain '8C' and resid 271 through 288 Processing helix chain '8C' and resid 422 through 424 No H-bonds generated for 'chain '8C' and resid 422 through 424' Processing helix chain '6A' and resid 26 through 50 removed outlier: 3.547A pdb=" N LEU6A 32 " --> pdb=" O ALA6A 28 " (cutoff:3.500A) Processing helix chain '6B' and resid 26 through 51 removed outlier: 3.545A pdb=" N LEU6B 32 " --> pdb=" O ALA6B 28 " (cutoff:3.500A) Processing helix chain '6C' and resid 26 through 51 removed outlier: 3.506A pdb=" N LEU6C 32 " --> pdb=" O ALA6C 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '8A' and resid 6 through 10 WARNING: can't find start of bonding for strands! previous: chain '8A' and resid 13 through 14 current: chain '8A' and resid 34 through 40 WARNING: can't find start of bonding for strands! previous: chain '8A' and resid 34 through 40 current: chain '8A' and resid 73 through 88 removed outlier: 6.834A pdb=" N THR8A 97 " --> pdb=" O VAL8A 81 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN8A 83 " --> pdb=" O THR8A 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR8A 95 " --> pdb=" O GLN8A 83 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU8A 85 " --> pdb=" O LEU8A 93 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU8A 93 " --> pdb=" O LEU8A 85 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE8A 87 " --> pdb=" O ASP8A 91 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP8A 91 " --> pdb=" O PHE8A 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '8A' and resid 91 through 99 current: chain '8A' and resid 320 through 332 removed outlier: 3.603A pdb=" N GLY8A 326 " --> pdb=" O THR8A 342 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '8A' and resid 336 through 343 current: chain '8B' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain '8B' and resid 13 through 14 current: chain '8B' and resid 34 through 40 WARNING: can't find start of bonding for strands! previous: chain '8B' and resid 34 through 40 current: chain '8B' and resid 73 through 88 removed outlier: 6.855A pdb=" N THR8B 97 " --> pdb=" O VAL8B 81 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN8B 83 " --> pdb=" O THR8B 95 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR8B 95 " --> pdb=" O GLN8B 83 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU8B 85 " --> pdb=" O LEU8B 93 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU8B 93 " --> pdb=" O LEU8B 85 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE8B 87 " --> pdb=" O ASP8B 91 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP8B 91 " --> pdb=" O PHE8B 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '8B' and resid 91 through 99 current: chain '8B' and resid 320 through 332 removed outlier: 3.625A pdb=" N GLY8B 326 " --> pdb=" O THR8B 342 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '8B' and resid 336 through 343 current: chain '8C' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain '8C' and resid 13 through 14 current: chain '8C' and resid 34 through 40 WARNING: can't find start of bonding for strands! previous: chain '8C' and resid 34 through 40 current: chain '8C' and resid 73 through 88 removed outlier: 6.798A pdb=" N THR8C 97 " --> pdb=" O VAL8C 81 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN8C 83 " --> pdb=" O THR8C 95 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR8C 95 " --> pdb=" O GLN8C 83 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU8C 85 " --> pdb=" O LEU8C 93 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU8C 93 " --> pdb=" O LEU8C 85 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE8C 87 " --> pdb=" O ASP8C 91 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP8C 91 " --> pdb=" O PHE8C 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '8C' and resid 91 through 99 current: chain '8C' and resid 320 through 332 removed outlier: 3.621A pdb=" N GLY8C 326 " --> pdb=" O THR8C 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '8A' and resid 110 through 118 removed outlier: 5.734A pdb=" N HIS8A 110 " --> pdb=" O ARG8A 153 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU8A 147 " --> pdb=" O LYS8A 116 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER8A 118 " --> pdb=" O VAL8A 145 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL8A 145 " --> pdb=" O SER8A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '8A' and resid 134 through 137 Processing sheet with id=AA4, first strand: chain '8A' and resid 220 through 227 Processing sheet with id=AA5, first strand: chain '8A' and resid 360 through 364 removed outlier: 7.040A pdb=" N PHE8A 392 " --> pdb=" O PRO8A 428 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE8A 430 " --> pdb=" O PHE8A 392 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG8A 394 " --> pdb=" O ILE8A 430 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY8A 432 " --> pdb=" O ARG8A 394 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE8A 417 " --> pdb=" O LEU8A 431 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER8A 433 " --> pdb=" O GLU8A 415 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLU8A 415 " --> pdb=" O SER8A 433 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '8A' and resid 400 through 401 WARNING: can't find start of bonding for strands! previous: chain '8A' and resid 404 through 407 current: chain '8A' and resid 463 through 468 removed outlier: 3.812A pdb=" N ASN8A 481 " --> pdb=" O SER8A 478 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '8A' and resid 491 through 494 current: chain '8B' and resid 404 through 407 WARNING: can't find start of bonding for strands! previous: chain '8B' and resid 404 through 407 current: chain '8B' and resid 461 through 468 removed outlier: 3.799A pdb=" N ASN8B 481 " --> pdb=" O SER8B 478 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '8B' and resid 491 through 494 current: chain '8C' and resid 404 through 407 WARNING: can't find start of bonding for strands! previous: chain '8C' and resid 404 through 407 current: chain '8C' and resid 463 through 468 removed outlier: 3.775A pdb=" N ASN8C 481 " --> pdb=" O SER8C 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '8A' and resid 522 through 524 removed outlier: 6.665A pdb=" N ASN8B 530 " --> pdb=" O ILE8A 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '8B' and resid 110 through 118 removed outlier: 5.842A pdb=" N HIS8B 110 " --> pdb=" O ARG8B 153 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU8B 147 " --> pdb=" O LYS8B 116 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER8B 118 " --> pdb=" O VAL8B 145 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL8B 145 " --> pdb=" O SER8B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '8B' and resid 134 through 137 Processing sheet with id=AB1, first strand: chain '8B' and resid 220 through 227 Processing sheet with id=AB2, first strand: chain '8B' and resid 360 through 364 removed outlier: 7.026A pdb=" N PHE8B 392 " --> pdb=" O PRO8B 428 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE8B 430 " --> pdb=" O PHE8B 392 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG8B 394 " --> pdb=" O ILE8B 430 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY8B 432 " --> pdb=" O ARG8B 394 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE8B 417 " --> pdb=" O LEU8B 431 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER8B 433 " --> pdb=" O GLU8B 415 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLU8B 415 " --> pdb=" O SER8B 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '8C' and resid 110 through 118 removed outlier: 5.878A pdb=" N HIS8C 110 " --> pdb=" O ARG8C 153 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU8C 147 " --> pdb=" O LYS8C 116 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER8C 118 " --> pdb=" O VAL8C 145 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL8C 145 " --> pdb=" O SER8C 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '8C' and resid 134 through 137 Processing sheet with id=AB5, first strand: chain '8C' and resid 237 through 239 Processing sheet with id=AB6, first strand: chain '8C' and resid 226 through 227 Processing sheet with id=AB7, first strand: chain '8C' and resid 360 through 364 removed outlier: 7.008A pdb=" N PHE8C 392 " --> pdb=" O PRO8C 428 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ILE8C 430 " --> pdb=" O PHE8C 392 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG8C 394 " --> pdb=" O ILE8C 430 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY8C 432 " --> pdb=" O ARG8C 394 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE8C 417 " --> pdb=" O LEU8C 431 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER8C 433 " --> pdb=" O GLU8C 415 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU8C 415 " --> pdb=" O SER8C 433 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 966 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: 1.98 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4350 1.34 - 1.46: 1999 1.46 - 1.57: 6776 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 13188 Sorted by residual: bond pdb=" CA GLY8A 479 " pdb=" C GLY8A 479 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.33e-02 5.65e+03 1.22e+00 bond pdb=" C ASN8B 436 " pdb=" N PRO8B 437 " ideal model delta sigma weight residual 1.336 1.346 -0.011 1.08e-02 8.57e+03 9.73e-01 bond pdb=" CB GLU8C 358 " pdb=" CG GLU8C 358 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.67e-01 bond pdb=" CB GLU8B 358 " pdb=" CG GLU8B 358 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.43e-01 bond pdb=" CB GLN8C 201 " pdb=" CG GLN8C 201 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.22e-01 ... (remaining 13183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 17660 1.96 - 3.92: 200 3.92 - 5.87: 19 5.87 - 7.83: 2 7.83 - 9.79: 2 Bond angle restraints: 17883 Sorted by residual: angle pdb=" N VAL8C 356 " pdb=" CA VAL8C 356 " pdb=" C VAL8C 356 " ideal model delta sigma weight residual 110.05 106.89 3.16 1.09e+00 8.42e-01 8.42e+00 angle pdb=" CG1 ILE8A 456 " pdb=" CB ILE8A 456 " pdb=" CG2 ILE8A 456 " ideal model delta sigma weight residual 110.70 102.02 8.68 3.00e+00 1.11e-01 8.37e+00 angle pdb=" CA LEU6C 37 " pdb=" CB LEU6C 37 " pdb=" CG LEU6C 37 " ideal model delta sigma weight residual 116.30 126.09 -9.79 3.50e+00 8.16e-02 7.82e+00 angle pdb=" N VAL8B 356 " pdb=" CA VAL8B 356 " pdb=" C VAL8B 356 " ideal model delta sigma weight residual 110.05 107.02 3.03 1.09e+00 8.42e-01 7.73e+00 angle pdb=" C GLN8B 71 " pdb=" CA GLN8B 71 " pdb=" CB GLN8B 71 " ideal model delta sigma weight residual 110.42 115.85 -5.43 1.99e+00 2.53e-01 7.43e+00 ... (remaining 17878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7001 17.88 - 35.75: 763 35.75 - 53.63: 220 53.63 - 71.51: 48 71.51 - 89.38: 29 Dihedral angle restraints: 8061 sinusoidal: 3261 harmonic: 4800 Sorted by residual: dihedral pdb=" CA LYS8C 357 " pdb=" C LYS8C 357 " pdb=" N GLU8C 358 " pdb=" CA GLU8C 358 " ideal model delta harmonic sigma weight residual 180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG8C 216 " pdb=" CD ARG8C 216 " pdb=" NE ARG8C 216 " pdb=" CZ ARG8C 216 " ideal model delta sinusoidal sigma weight residual 90.00 41.05 48.95 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG8B 216 " pdb=" CD ARG8B 216 " pdb=" NE ARG8B 216 " pdb=" CZ ARG8B 216 " ideal model delta sinusoidal sigma weight residual 90.00 41.12 48.88 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 8058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1487 0.042 - 0.085: 383 0.085 - 0.127: 189 0.127 - 0.170: 13 0.170 - 0.212: 1 Chirality restraints: 2073 Sorted by residual: chirality pdb=" CB ILE8A 456 " pdb=" CA ILE8A 456 " pdb=" CG1 ILE8A 456 " pdb=" CG2 ILE8A 456 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE8C 6 " pdb=" N ILE8C 6 " pdb=" C ILE8C 6 " pdb=" CB ILE8C 6 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE8B 456 " pdb=" N ILE8B 456 " pdb=" C ILE8B 456 " pdb=" CB ILE8B 456 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 2070 not shown) Planarity restraints: 2331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS8B 100 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO8B 101 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO8B 101 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO8B 101 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS8C 100 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO8C 101 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO8C 101 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO8C 101 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS8A 100 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO8A 101 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO8A 101 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO8A 101 " -0.021 5.00e-02 4.00e+02 ... (remaining 2328 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 219 2.67 - 3.23: 11656 3.23 - 3.79: 19033 3.79 - 4.34: 27505 4.34 - 4.90: 46076 Nonbonded interactions: 104489 Sorted by model distance: nonbonded pdb=" OG SER8A 520 " pdb=" O LYS8C 512 " model vdw 2.118 3.040 nonbonded pdb=" N GLN8C 201 " pdb=" OE1 GLN8C 201 " model vdw 2.196 3.120 nonbonded pdb=" N GLN8A 201 " pdb=" OE1 GLN8A 201 " model vdw 2.217 3.120 nonbonded pdb=" O GLU6A 30 " pdb=" ND2 ASN6A 34 " model vdw 2.231 3.120 nonbonded pdb=" O LYS8A 512 " pdb=" OG SER8B 520 " model vdw 2.245 3.040 ... (remaining 104484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain '6A' selection = chain '6B' selection = chain '6C' } ncs_group { reference = chain '8A' selection = chain '8B' selection = chain '8C' } 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: 4.930 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.460 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 0.003 0.030 13188 Z= 0.127 Angle : 0.531 9.790 17883 Z= 0.283 Chirality : 0.045 0.212 2073 Planarity : 0.003 0.039 2331 Dihedral : 17.230 89.383 4941 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.44 % Allowed : 21.65 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1647 helix: 1.39 (0.31), residues: 249 sheet: 1.02 (0.21), residues: 618 loop : -0.53 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG8A 216 TYR 0.012 0.001 TYR8C 277 PHE 0.007 0.001 PHE8C 408 TRP 0.010 0.001 TRP8A 264 HIS 0.004 0.001 HIS8A 461 Details of bonding type rmsd covalent geometry : bond 0.00290 (13188) covalent geometry : angle 0.53148 (17883) hydrogen bonds : bond 0.22628 ( 375) hydrogen bonds : angle 7.21558 ( 966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.494 Fit side-chains REVERT: 8A 515 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8641 (p) REVERT: 8A 523 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: 8B 493 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8520 (tt) REVERT: 8B 515 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8637 (p) REVERT: 8C 149 MET cc_start: 0.9296 (tpt) cc_final: 0.9021 (tpp) REVERT: 8C 216 ARG cc_start: 0.8639 (mtp85) cc_final: 0.8272 (mtp180) REVERT: 8C 394 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8000 (mtm180) outliers start: 21 outliers final: 12 residues processed: 117 average time/residue: 0.6393 time to fit residues: 81.4925 Evaluate side-chains 108 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 348 ASP Chi-restraints excluded: chain 8A residue 515 SER Chi-restraints excluded: chain 8A residue 523 ASP Chi-restraints excluded: chain 8B residue 3 ILE Chi-restraints excluded: chain 8B residue 75 LEU Chi-restraints excluded: chain 8B residue 113 LEU Chi-restraints excluded: chain 8B residue 345 MET Chi-restraints excluded: chain 8B residue 493 LEU Chi-restraints excluded: chain 8B residue 501 THR Chi-restraints excluded: chain 8B residue 515 SER Chi-restraints excluded: chain 8B residue 523 ASP Chi-restraints excluded: chain 8C residue 22 ASN Chi-restraints excluded: chain 8C residue 50 ASP Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 8C residue 394 ARG Chi-restraints excluded: chain 8C residue 523 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8A 469 ASN 8B 90 GLN 8C 22 ASN 8C 90 GLN 8C 469 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.072198 restraints weight = 21537.463| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.37 r_work: 0.2681 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13188 Z= 0.110 Angle : 0.517 7.214 17883 Z= 0.273 Chirality : 0.046 0.186 2073 Planarity : 0.004 0.043 2331 Dihedral : 6.207 109.681 1758 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.27 % Allowed : 19.52 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.85 (0.20), residues: 1647 helix: 1.96 (0.31), residues: 264 sheet: 1.27 (0.21), residues: 594 loop : -0.48 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG8A 216 TYR 0.008 0.001 TYR8C 277 PHE 0.008 0.001 PHE8B 467 TRP 0.006 0.001 TRP8A 264 HIS 0.004 0.001 HIS8B 461 Details of bonding type rmsd covalent geometry : bond 0.00240 (13188) covalent geometry : angle 0.51662 (17883) hydrogen bonds : bond 0.05412 ( 375) hydrogen bonds : angle 5.21463 ( 966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: 8A 438 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8633 (tptt) REVERT: 8B 411 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8660 (mm-30) REVERT: 8C 216 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8371 (mtp180) REVERT: 8C 359 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8661 (mt) REVERT: 6B 46 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6621 (tt) outliers start: 33 outliers final: 9 residues processed: 124 average time/residue: 0.6494 time to fit residues: 87.7201 Evaluate side-chains 97 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 3 ILE Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 79 ILE Chi-restraints excluded: chain 8A residue 438 LYS Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 411 GLU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8C residue 22 ASN Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 8C residue 359 LEU Chi-restraints excluded: chain 6B residue 38 ILE Chi-restraints excluded: chain 6B residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8A 449 ASN 8B 90 GLN 8C 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.070712 restraints weight = 21699.437| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.38 r_work: 0.2660 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13188 Z= 0.164 Angle : 0.516 6.812 17883 Z= 0.270 Chirality : 0.047 0.154 2073 Planarity : 0.004 0.043 2331 Dihedral : 4.727 48.162 1728 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.96 % Allowed : 18.83 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1647 helix: 1.98 (0.31), residues: 264 sheet: 1.21 (0.21), residues: 591 loop : -0.54 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG8B 216 TYR 0.011 0.001 TYR8C 277 PHE 0.008 0.001 PHE8B 467 TRP 0.006 0.001 TRP8B 212 HIS 0.004 0.001 HIS8B 100 Details of bonding type rmsd covalent geometry : bond 0.00388 (13188) covalent geometry : angle 0.51591 (17883) hydrogen bonds : bond 0.05138 ( 375) hydrogen bonds : angle 4.94070 ( 966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: 8A 73 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8677 (p) REVERT: 8A 438 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8730 (tptt) REVERT: 8B 73 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8658 (t) REVERT: 8B 153 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8968 (mtt180) REVERT: 8B 359 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8905 (mp) REVERT: 8C 73 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8634 (t) REVERT: 8C 359 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8818 (mt) outliers start: 43 outliers final: 18 residues processed: 126 average time/residue: 0.6471 time to fit residues: 89.1982 Evaluate side-chains 106 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 3 ILE Chi-restraints excluded: chain 8A residue 5 GLU Chi-restraints excluded: chain 8A residue 19 THR Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 73 THR Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 190 THR Chi-restraints excluded: chain 8A residue 424 ASP Chi-restraints excluded: chain 8A residue 438 LYS Chi-restraints excluded: chain 8A residue 501 THR Chi-restraints excluded: chain 8B residue 3 ILE Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 73 THR Chi-restraints excluded: chain 8B residue 113 LEU Chi-restraints excluded: chain 8B residue 153 ARG Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 359 LEU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8B residue 492 THR Chi-restraints excluded: chain 8C residue 22 ASN Chi-restraints excluded: chain 8C residue 57 LEU Chi-restraints excluded: chain 8C residue 73 THR Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 8C residue 359 LEU Chi-restraints excluded: chain 6B residue 38 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8B 90 GLN 8C 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.087528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.069683 restraints weight = 21757.039| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.36 r_work: 0.2639 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13188 Z= 0.211 Angle : 0.549 10.211 17883 Z= 0.285 Chirality : 0.048 0.266 2073 Planarity : 0.004 0.041 2331 Dihedral : 4.895 49.321 1728 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.30 % Allowed : 18.69 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.68 (0.20), residues: 1647 helix: 2.07 (0.31), residues: 255 sheet: 1.07 (0.21), residues: 594 loop : -0.58 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG8C 216 TYR 0.015 0.001 TYR8C 277 PHE 0.010 0.001 PHE8C 408 TRP 0.008 0.001 TRP8B 212 HIS 0.005 0.001 HIS8B 461 Details of bonding type rmsd covalent geometry : bond 0.00508 (13188) covalent geometry : angle 0.54904 (17883) hydrogen bonds : bond 0.05000 ( 375) hydrogen bonds : angle 4.90908 ( 966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 86 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: 8A 73 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8638 (p) REVERT: 8A 438 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8821 (tptt) REVERT: 8A 480 LYS cc_start: 0.9314 (mmpt) cc_final: 0.9090 (mmtm) REVERT: 8B 359 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8883 (mp) REVERT: 8C 73 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8620 (t) outliers start: 48 outliers final: 27 residues processed: 131 average time/residue: 0.6250 time to fit residues: 89.5871 Evaluate side-chains 109 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 3 ILE Chi-restraints excluded: chain 8A residue 19 THR Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 73 THR Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 79 ILE Chi-restraints excluded: chain 8A residue 190 THR Chi-restraints excluded: chain 8A residue 236 THR Chi-restraints excluded: chain 8A residue 438 LYS Chi-restraints excluded: chain 8A residue 492 THR Chi-restraints excluded: chain 8A residue 501 THR Chi-restraints excluded: chain 8B residue 3 ILE Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 113 LEU Chi-restraints excluded: chain 8B residue 169 THR Chi-restraints excluded: chain 8B residue 190 THR Chi-restraints excluded: chain 8B residue 294 SER Chi-restraints excluded: chain 8B residue 345 MET Chi-restraints excluded: chain 8B residue 348 ASP Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 359 LEU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8B residue 456 ILE Chi-restraints excluded: chain 8B residue 492 THR Chi-restraints excluded: chain 8C residue 22 ASN Chi-restraints excluded: chain 8C residue 73 THR Chi-restraints excluded: chain 8C residue 190 THR Chi-restraints excluded: chain 8C residue 209 ASN Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 8C residue 501 THR Chi-restraints excluded: chain 6B residue 38 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8B 90 GLN 8C 90 GLN 8C 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.087890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.069899 restraints weight = 21741.382| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.37 r_work: 0.2647 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13188 Z= 0.163 Angle : 0.518 7.860 17883 Z= 0.269 Chirality : 0.047 0.207 2073 Planarity : 0.004 0.041 2331 Dihedral : 4.856 49.966 1728 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.02 % Allowed : 19.45 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.65 (0.20), residues: 1647 helix: 2.04 (0.31), residues: 258 sheet: 1.08 (0.21), residues: 591 loop : -0.61 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG8B 216 TYR 0.012 0.001 TYR8B 277 PHE 0.009 0.001 PHE8C 408 TRP 0.006 0.001 TRP8A 226 HIS 0.005 0.001 HIS8B 461 Details of bonding type rmsd covalent geometry : bond 0.00387 (13188) covalent geometry : angle 0.51806 (17883) hydrogen bonds : bond 0.04672 ( 375) hydrogen bonds : angle 4.81889 ( 966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 83 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: 8A 73 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8650 (p) REVERT: 8A 438 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8827 (tptt) REVERT: 8A 480 LYS cc_start: 0.9322 (mmpt) cc_final: 0.9087 (mmtm) REVERT: 8B 359 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8836 (mp) REVERT: 8B 411 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8741 (mm-30) REVERT: 8B 493 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8739 (tt) REVERT: 8C 73 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8617 (t) REVERT: 8C 82 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8786 (ttp80) REVERT: 8C 345 MET cc_start: 0.9089 (mtp) cc_final: 0.8806 (mtp) outliers start: 44 outliers final: 25 residues processed: 123 average time/residue: 0.6417 time to fit residues: 86.2315 Evaluate side-chains 110 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 3 ILE Chi-restraints excluded: chain 8A residue 5 GLU Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 73 THR Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 79 ILE Chi-restraints excluded: chain 8A residue 190 THR Chi-restraints excluded: chain 8A residue 236 THR Chi-restraints excluded: chain 8A residue 424 ASP Chi-restraints excluded: chain 8A residue 438 LYS Chi-restraints excluded: chain 8A residue 492 THR Chi-restraints excluded: chain 8A residue 501 THR Chi-restraints excluded: chain 8B residue 3 ILE Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 113 LEU Chi-restraints excluded: chain 8B residue 190 THR Chi-restraints excluded: chain 8B residue 294 SER Chi-restraints excluded: chain 8B residue 345 MET Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 359 LEU Chi-restraints excluded: chain 8B residue 411 GLU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8B residue 492 THR Chi-restraints excluded: chain 8B residue 493 LEU Chi-restraints excluded: chain 8C residue 22 ASN Chi-restraints excluded: chain 8C residue 57 LEU Chi-restraints excluded: chain 8C residue 73 THR Chi-restraints excluded: chain 8C residue 82 ARG Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 8C residue 492 THR Chi-restraints excluded: chain 8C residue 501 THR Chi-restraints excluded: chain 6B residue 38 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8B 90 GLN 8C 90 GLN 6A 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.086793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.068961 restraints weight = 21734.664| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.34 r_work: 0.2629 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13188 Z= 0.232 Angle : 0.552 7.783 17883 Z= 0.287 Chirality : 0.048 0.195 2073 Planarity : 0.004 0.042 2331 Dihedral : 4.966 50.378 1728 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.57 % Allowed : 19.45 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1647 helix: 2.05 (0.31), residues: 255 sheet: 1.00 (0.21), residues: 591 loop : -0.61 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG8C 216 TYR 0.014 0.001 TYR8B 277 PHE 0.012 0.001 PHE8C 408 TRP 0.008 0.001 TRP8B 212 HIS 0.006 0.001 HIS8B 461 Details of bonding type rmsd covalent geometry : bond 0.00559 (13188) covalent geometry : angle 0.55210 (17883) hydrogen bonds : bond 0.04911 ( 375) hydrogen bonds : angle 4.85581 ( 966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 82 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: 8A 73 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8628 (p) REVERT: 8B 359 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8860 (mp) REVERT: 8B 493 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8805 (tt) REVERT: 8C 73 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8624 (t) REVERT: 8C 82 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8775 (ttp80) REVERT: 8C 345 MET cc_start: 0.9183 (mtp) cc_final: 0.8913 (mtp) outliers start: 52 outliers final: 31 residues processed: 130 average time/residue: 0.6204 time to fit residues: 88.3042 Evaluate side-chains 115 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 3 ILE Chi-restraints excluded: chain 8A residue 5 GLU Chi-restraints excluded: chain 8A residue 19 THR Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 73 THR Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 79 ILE Chi-restraints excluded: chain 8A residue 160 LEU Chi-restraints excluded: chain 8A residue 190 THR Chi-restraints excluded: chain 8A residue 236 THR Chi-restraints excluded: chain 8A residue 386 LEU Chi-restraints excluded: chain 8A residue 492 THR Chi-restraints excluded: chain 8A residue 501 THR Chi-restraints excluded: chain 8B residue 3 ILE Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 113 LEU Chi-restraints excluded: chain 8B residue 169 THR Chi-restraints excluded: chain 8B residue 190 THR Chi-restraints excluded: chain 8B residue 294 SER Chi-restraints excluded: chain 8B residue 345 MET Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 359 LEU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8B residue 492 THR Chi-restraints excluded: chain 8B residue 493 LEU Chi-restraints excluded: chain 8C residue 22 ASN Chi-restraints excluded: chain 8C residue 57 LEU Chi-restraints excluded: chain 8C residue 73 THR Chi-restraints excluded: chain 8C residue 82 ARG Chi-restraints excluded: chain 8C residue 190 THR Chi-restraints excluded: chain 8C residue 209 ASN Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 8C residue 492 THR Chi-restraints excluded: chain 8C residue 501 THR Chi-restraints excluded: chain 8C residue 515 SER Chi-restraints excluded: chain 6B residue 38 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 103 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8B 90 GLN 8B 267 ASN 8C 90 GLN 8C 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.071763 restraints weight = 21352.173| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.34 r_work: 0.2672 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13188 Z= 0.093 Angle : 0.490 6.326 17883 Z= 0.256 Chirality : 0.045 0.163 2073 Planarity : 0.004 0.043 2331 Dihedral : 4.661 41.897 1728 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.27 % Allowed : 20.69 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1647 helix: 1.98 (0.31), residues: 264 sheet: 1.06 (0.21), residues: 591 loop : -0.57 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG8C 216 TYR 0.007 0.001 TYR8B 277 PHE 0.007 0.001 PHE8C 87 TRP 0.006 0.001 TRP8A 264 HIS 0.004 0.001 HIS8B 461 Details of bonding type rmsd covalent geometry : bond 0.00206 (13188) covalent geometry : angle 0.48968 (17883) hydrogen bonds : bond 0.04138 ( 375) hydrogen bonds : angle 4.64135 ( 966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: 8A 394 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.9059 (mmm160) REVERT: 8B 411 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8672 (mm-30) REVERT: 8B 493 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8803 (tt) REVERT: 8C 73 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8618 (t) REVERT: 8C 345 MET cc_start: 0.9173 (mtp) cc_final: 0.8846 (mtp) outliers start: 33 outliers final: 14 residues processed: 117 average time/residue: 0.6203 time to fit residues: 79.5316 Evaluate side-chains 99 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 5 GLU Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 79 ILE Chi-restraints excluded: chain 8A residue 386 LEU Chi-restraints excluded: chain 8A residue 394 ARG Chi-restraints excluded: chain 8A residue 455 VAL Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 113 LEU Chi-restraints excluded: chain 8B residue 345 MET Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 411 GLU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8B residue 493 LEU Chi-restraints excluded: chain 8C residue 73 THR Chi-restraints excluded: chain 8C residue 209 ASN Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 6B residue 38 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 158 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8B 90 GLN 8C 22 ASN 8C 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.087146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.068942 restraints weight = 21386.345| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.35 r_work: 0.2621 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13188 Z= 0.231 Angle : 0.557 11.791 17883 Z= 0.289 Chirality : 0.048 0.246 2073 Planarity : 0.004 0.043 2331 Dihedral : 4.736 31.014 1726 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.34 % Allowed : 21.17 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1647 helix: 2.14 (0.31), residues: 252 sheet: 0.95 (0.21), residues: 591 loop : -0.61 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG8C 216 TYR 0.016 0.001 TYR8B 277 PHE 0.011 0.001 PHE8C 408 TRP 0.007 0.001 TRP8B 212 HIS 0.006 0.001 HIS8B 461 Details of bonding type rmsd covalent geometry : bond 0.00559 (13188) covalent geometry : angle 0.55720 (17883) hydrogen bonds : bond 0.04682 ( 375) hydrogen bonds : angle 4.78238 ( 966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: 8B 411 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8687 (mm-30) REVERT: 8B 493 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8710 (tt) REVERT: 8C 73 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8528 (t) REVERT: 8C 82 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8814 (tpp80) REVERT: 8C 345 MET cc_start: 0.9194 (mtp) cc_final: 0.8845 (mtp) REVERT: 8C 493 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8720 (tt) outliers start: 34 outliers final: 21 residues processed: 114 average time/residue: 0.6156 time to fit residues: 76.8655 Evaluate side-chains 105 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 5 GLU Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 79 ILE Chi-restraints excluded: chain 8A residue 160 LEU Chi-restraints excluded: chain 8A residue 236 THR Chi-restraints excluded: chain 8A residue 455 VAL Chi-restraints excluded: chain 8A residue 492 THR Chi-restraints excluded: chain 8B residue 3 ILE Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 169 THR Chi-restraints excluded: chain 8B residue 190 THR Chi-restraints excluded: chain 8B residue 345 MET Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 411 GLU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8B residue 493 LEU Chi-restraints excluded: chain 8C residue 22 ASN Chi-restraints excluded: chain 8C residue 73 THR Chi-restraints excluded: chain 8C residue 82 ARG Chi-restraints excluded: chain 8C residue 190 THR Chi-restraints excluded: chain 8C residue 209 ASN Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 8C residue 492 THR Chi-restraints excluded: chain 8C residue 493 LEU Chi-restraints excluded: chain 6B residue 38 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 5.9990 chunk 44 optimal weight: 0.0370 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8B 90 GLN 8C 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.089891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.071587 restraints weight = 21243.527| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.38 r_work: 0.2670 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13188 Z= 0.095 Angle : 0.506 8.582 17883 Z= 0.264 Chirality : 0.046 0.183 2073 Planarity : 0.004 0.043 2331 Dihedral : 4.506 27.138 1726 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.58 % Allowed : 22.06 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1647 helix: 2.20 (0.31), residues: 255 sheet: 0.99 (0.21), residues: 591 loop : -0.59 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG8C 216 TYR 0.006 0.001 TYR8B 277 PHE 0.006 0.001 PHE8B 467 TRP 0.007 0.001 TRP8A 264 HIS 0.003 0.001 HIS8B 461 Details of bonding type rmsd covalent geometry : bond 0.00214 (13188) covalent geometry : angle 0.50646 (17883) hydrogen bonds : bond 0.04062 ( 375) hydrogen bonds : angle 4.61156 ( 966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: 8A 201 GLN cc_start: 0.8506 (pm20) cc_final: 0.8283 (mp10) REVERT: 8B 201 GLN cc_start: 0.8458 (pm20) cc_final: 0.8114 (mp-120) REVERT: 8B 411 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8604 (mm-30) REVERT: 8B 493 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8737 (tt) REVERT: 8C 345 MET cc_start: 0.9204 (mtp) cc_final: 0.8808 (mtp) outliers start: 23 outliers final: 15 residues processed: 105 average time/residue: 0.6837 time to fit residues: 78.1131 Evaluate side-chains 96 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 5 GLU Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 79 ILE Chi-restraints excluded: chain 8A residue 386 LEU Chi-restraints excluded: chain 8A residue 455 VAL Chi-restraints excluded: chain 8A residue 458 GLN Chi-restraints excluded: chain 8B residue 3 ILE Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 169 THR Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 411 GLU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8B residue 493 LEU Chi-restraints excluded: chain 8C residue 209 ASN Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 6B residue 38 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 89 optimal weight: 0.0170 chunk 91 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8A 461 HIS 8B 90 GLN 8B 360 HIS 8C 22 ASN 8C 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.087326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.069085 restraints weight = 21574.717| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.37 r_work: 0.2613 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13188 Z= 0.257 Angle : 0.581 11.362 17883 Z= 0.301 Chirality : 0.049 0.237 2073 Planarity : 0.004 0.054 2331 Dihedral : 4.778 31.306 1726 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.86 % Allowed : 21.92 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.20), residues: 1647 helix: 2.09 (0.31), residues: 252 sheet: 0.85 (0.21), residues: 594 loop : -0.61 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG8C 216 TYR 0.019 0.002 TYR8B 277 PHE 0.012 0.001 PHE8C 408 TRP 0.008 0.001 TRP8B 212 HIS 0.006 0.001 HIS8B 100 Details of bonding type rmsd covalent geometry : bond 0.00621 (13188) covalent geometry : angle 0.58081 (17883) hydrogen bonds : bond 0.04817 ( 375) hydrogen bonds : angle 4.81340 ( 966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3294 Ramachandran restraints generated. 1647 Oldfield, 0 Emsley, 1647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: 8B 411 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8691 (mm-30) REVERT: 8B 493 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8727 (tt) REVERT: 8C 345 MET cc_start: 0.9215 (mtp) cc_final: 0.8838 (mtp) outliers start: 27 outliers final: 21 residues processed: 109 average time/residue: 0.6272 time to fit residues: 74.8910 Evaluate side-chains 102 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8A residue 3 ILE Chi-restraints excluded: chain 8A residue 5 GLU Chi-restraints excluded: chain 8A residue 57 LEU Chi-restraints excluded: chain 8A residue 75 LEU Chi-restraints excluded: chain 8A residue 79 ILE Chi-restraints excluded: chain 8A residue 236 THR Chi-restraints excluded: chain 8A residue 455 VAL Chi-restraints excluded: chain 8A residue 492 THR Chi-restraints excluded: chain 8B residue 3 ILE Chi-restraints excluded: chain 8B residue 57 LEU Chi-restraints excluded: chain 8B residue 113 LEU Chi-restraints excluded: chain 8B residue 169 THR Chi-restraints excluded: chain 8B residue 190 THR Chi-restraints excluded: chain 8B residue 356 VAL Chi-restraints excluded: chain 8B residue 411 GLU Chi-restraints excluded: chain 8B residue 455 VAL Chi-restraints excluded: chain 8B residue 493 LEU Chi-restraints excluded: chain 8C residue 209 ASN Chi-restraints excluded: chain 8C residue 356 VAL Chi-restraints excluded: chain 8C residue 371 SER Chi-restraints excluded: chain 8C residue 492 THR Chi-restraints excluded: chain 8C residue 515 SER Chi-restraints excluded: chain 6B residue 38 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 156 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8B 90 GLN 8C 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.090246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.071995 restraints weight = 21076.149| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.38 r_work: 0.2679 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13188 Z= 0.094 Angle : 0.505 8.328 17883 Z= 0.264 Chirality : 0.045 0.179 2073 Planarity : 0.004 0.044 2331 Dihedral : 4.447 25.172 1726 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.31 % Allowed : 22.47 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.62 (0.20), residues: 1647 helix: 2.07 (0.32), residues: 261 sheet: 0.95 (0.21), residues: 591 loop : -0.56 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG8C 216 TYR 0.011 0.001 TYR8C 277 PHE 0.006 0.001 PHE8B 467 TRP 0.008 0.001 TRP8A 264 HIS 0.004 0.001 HIS8B 461 Details of bonding type rmsd covalent geometry : bond 0.00212 (13188) covalent geometry : angle 0.50487 (17883) hydrogen bonds : bond 0.03942 ( 375) hydrogen bonds : angle 4.57148 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3987.89 seconds wall clock time: 69 minutes 7.67 seconds (4147.67 seconds total)