Starting phenix.real_space_refine on Sun Oct 25 04:24:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29tc_57359/10_2026/29tc_57359.cif Found real_map, /net/cci-nas-00/data/ceres_data/29tc_57359/10_2026/29tc_57359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/29tc_57359/10_2026/29tc_57359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29tc_57359/10_2026/29tc_57359.map" model { file = "/net/cci-nas-00/data/ceres_data/29tc_57359/10_2026/29tc_57359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29tc_57359/10_2026/29tc_57359.cif" } resolution = 2.54 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= 0.007 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 102 5.16 5 C 10164 2.51 5 N 2436 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15342 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2557 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 3 Chain: "B" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2557 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 3 Chain: "C" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2557 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 3 Chain: "D" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2557 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 3 Chain: "E" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2557 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 3 Chain: "F" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2557 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 3 Time building chain proxies: 2.93, per 1000 atoms: 0.19 Number of scatterers: 15342 At special positions: 0 Unit cell: (102.207, 107.415, 120.435, 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 102 16.00 O 2640 8.00 N 2436 7.00 C 10164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 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: 1.06 Conformation dependent library (CDL) restraints added in 738.6 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 8 sheets defined 77.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.755A pdb=" N ARG A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 169 through 179 removed outlier: 3.653A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 314 through 347 removed outlier: 3.746A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.621A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 383 through 393 removed outlier: 4.045A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.777A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.747A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.532A pdb=" N VAL B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.912A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.697A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 383 Processing helix chain 'B' and resid 383 through 393 removed outlier: 4.312A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.765A pdb=" N ARG C 18 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 146 through 165 removed outlier: 3.731A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 179 removed outlier: 3.567A pdb=" N VAL C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 314 through 347 removed outlier: 3.575A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 removed outlier: 3.687A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 383 Processing helix chain 'C' and resid 383 through 393 removed outlier: 4.303A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.755A pdb=" N ARG D 18 " --> pdb=" O PRO D 15 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 141 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.739A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 179 removed outlier: 3.579A pdb=" N VAL D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 314 through 347 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.693A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 383 removed outlier: 3.506A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 393 removed outlier: 4.293A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.801A pdb=" N ARG E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 21 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.719A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 179 removed outlier: 3.561A pdb=" N VAL E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 314 through 347 removed outlier: 3.600A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.665A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 383 Processing helix chain 'E' and resid 383 through 393 removed outlier: 4.320A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 21 removed outlier: 3.745A pdb=" N ARG F 18 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 141 Proline residue: F 126 - end of helix Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.512A pdb=" N LYS F 145 " --> pdb=" O ASN F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.698A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 179 removed outlier: 3.628A pdb=" N VAL F 177 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 314 through 347 removed outlier: 3.667A pdb=" N SER F 347 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.666A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 383 Processing helix chain 'F' and resid 383 through 393 removed outlier: 4.297A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AA8, first strand: chain 'F' and resid 53 through 56 1042 hydrogen bonds defined for protein. 3081 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: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4524 1.34 - 1.46: 4270 1.46 - 1.58: 6842 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 15780 Sorted by residual: bond pdb=" CB GLU E 236 " pdb=" CG GLU E 236 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CB GLU F 236 " pdb=" CG GLU F 236 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB GLN F 239 " pdb=" CG GLN F 239 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB GLN E 239 " pdb=" CG GLN E 239 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CB GLN D 239 " pdb=" CG GLN D 239 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 ... (remaining 15775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 21019 1.42 - 2.84: 282 2.84 - 4.26: 41 4.26 - 5.68: 22 5.68 - 7.10: 2 Bond angle restraints: 21366 Sorted by residual: angle pdb=" CA LYS B 235 " pdb=" CB LYS B 235 " pdb=" CG LYS B 235 " ideal model delta sigma weight residual 114.10 119.80 -5.70 2.00e+00 2.50e-01 8.11e+00 angle pdb=" CA LYS D 235 " pdb=" CB LYS D 235 " pdb=" CG LYS D 235 " ideal model delta sigma weight residual 114.10 119.72 -5.62 2.00e+00 2.50e-01 7.90e+00 angle pdb=" CA LYS D 62 " pdb=" CB LYS D 62 " pdb=" CG LYS D 62 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.31e+00 angle pdb=" C LYS E 369 " pdb=" N ASN E 370 " pdb=" CA ASN E 370 " ideal model delta sigma weight residual 122.42 118.27 4.15 1.55e+00 4.16e-01 7.16e+00 angle pdb=" CB GLN E 239 " pdb=" CG GLN E 239 " pdb=" CD GLN E 239 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.70e+00 3.46e-01 6.80e+00 ... (remaining 21361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.45: 8262 14.45 - 28.90: 626 28.90 - 43.35: 290 43.35 - 57.79: 77 57.79 - 72.24: 15 Dihedral angle restraints: 9270 sinusoidal: 3786 harmonic: 5484 Sorted by residual: dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual 93.00 45.03 47.97 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CB CYS C 57 " pdb=" SG CYS C 57 " pdb=" SG CYS C 65 " pdb=" CB CYS C 65 " ideal model delta sinusoidal sigma weight residual 93.00 48.54 44.46 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 65 " pdb=" CB CYS A 65 " ideal model delta sinusoidal sigma weight residual 93.00 49.59 43.41 1 1.00e+01 1.00e-02 2.63e+01 ... (remaining 9267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1374 0.026 - 0.051: 617 0.051 - 0.077: 262 0.077 - 0.103: 58 0.103 - 0.128: 47 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CA PRO A 147 " pdb=" N PRO A 147 " pdb=" C PRO A 147 " pdb=" CB PRO A 147 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA PRO B 147 " pdb=" N PRO B 147 " pdb=" C PRO B 147 " pdb=" CB PRO B 147 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA PRO D 147 " pdb=" N PRO D 147 " pdb=" C PRO D 147 " pdb=" CB PRO D 147 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 2355 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 63 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C ASP E 63 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP E 63 " 0.011 2.00e-02 2.50e+03 pdb=" N SER E 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 358 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" CD GLU A 358 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU A 358 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 358 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 365 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 366 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " -0.018 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 8367 3.01 - 3.48: 15945 3.48 - 3.95: 25472 3.95 - 4.43: 29705 4.43 - 4.90: 47114 Nonbonded interactions: 126603 Sorted by model distance: nonbonded pdb=" O ASP E 63 " pdb=" OD1 ASP E 63 " model vdw 2.537 3.040 nonbonded pdb=" O ASP C 63 " pdb=" OD1 ASP C 63 " model vdw 2.553 3.040 nonbonded pdb=" O ASP A 63 " pdb=" OD2 ASP A 63 " model vdw 2.561 3.040 nonbonded pdb=" O GLN D 239 " pdb=" OE1 GLN D 239 " model vdw 2.600 3.040 nonbonded pdb=" O ASP A 25 " pdb=" OD1 ASP A 29 " model vdw 2.603 3.040 ... (remaining 126598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 11.490 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.730 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 0.037 15798 Z= 0.124 Angle : 0.459 7.100 21402 Z= 0.253 Chirality : 0.037 0.128 2358 Planarity : 0.003 0.033 2568 Dihedral : 13.351 72.243 5664 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.35 % Allowed : 19.08 % Favored : 79.56 % 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: 1.18 (0.19), residues: 1782 helix: 1.12 (0.14), residues: 1290 sheet: 1.85 (0.53), residues: 108 loop : -0.46 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 18 TYR 0.012 0.001 TYR A 351 PHE 0.009 0.001 PHE A 41 TRP 0.014 0.001 TRP B 168 HIS 0.003 0.001 HIS D 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (15780) covalent geometry : angle 0.45739 / 0.25 (21366) SS BOND : bond 0.00162 / 0.10 ( 18) SS BOND : angle 1.06721 / 0.68 ( 36) hydrogen bonds : bond 0.15505 / 10.61 ( 1042) hydrogen bonds : angle 6.55938 / 4.70 ( 3081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.662 Fit side-chains REVERT: A 154 GLU cc_start: 0.8209 (tt0) cc_final: 0.7994 (tt0) REVERT: A 235 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8181 (tmmt) REVERT: B 154 GLU cc_start: 0.8325 (tt0) cc_final: 0.8113 (tt0) REVERT: C 154 GLU cc_start: 0.8307 (tt0) cc_final: 0.8048 (tt0) REVERT: C 235 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8377 (tptp) REVERT: D 154 GLU cc_start: 0.8337 (tt0) cc_final: 0.8127 (tt0) REVERT: E 154 GLU cc_start: 0.8403 (tt0) cc_final: 0.8173 (tt0) REVERT: E 383 ASP cc_start: 0.8481 (t0) cc_final: 0.8238 (t0) REVERT: F 154 GLU cc_start: 0.8291 (tt0) cc_final: 0.8055 (tt0) REVERT: F 235 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8006 (tmmm) REVERT: F 236 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8540 (mm-30) REVERT: F 383 ASP cc_start: 0.8394 (t0) cc_final: 0.8164 (t0) outliers start: 23 outliers final: 12 residues processed: 106 average time/residue: 0.6468 time to fit residues: 75.5402 Evaluate side-chains 99 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 275 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.9593 > 50:) chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN D 49 GLN E 49 GLN F 49 GLN F 141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088337 restraints weight = 27698.169| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.59 r_work: 0.3127 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15798 Z= 0.146 Angle : 0.463 5.363 21402 Z= 0.256 Chirality : 0.039 0.134 2358 Planarity : 0.003 0.028 2568 Dihedral : 5.405 47.458 2052 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.77 % Allowed : 18.14 % Favored : 79.09 % 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: 2.20 (0.20), residues: 1782 helix: 2.00 (0.14), residues: 1302 sheet: 1.61 (0.50), residues: 108 loop : -0.50 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 18 TYR 0.016 0.001 TYR C 30 PHE 0.015 0.001 PHE F 41 TRP 0.012 0.001 TRP A 24 HIS 0.003 0.001 HIS F 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (15780) covalent geometry : angle 0.46180 / 0.26 (21366) SS BOND : bond 0.00188 / 0.11 ( 18) SS BOND : angle 1.06308 / 0.68 ( 36) hydrogen bonds : bond 0.04052 / 2.71 ( 1042) hydrogen bonds : angle 4.47216 / 3.22 ( 3081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 0.596 Fit side-chains REVERT: A 154 GLU cc_start: 0.8183 (tt0) cc_final: 0.7967 (tt0) REVERT: A 241 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7973 (mtmp) REVERT: B 154 GLU cc_start: 0.8242 (tt0) cc_final: 0.8030 (tt0) REVERT: B 383 ASP cc_start: 0.8112 (t0) cc_final: 0.7862 (t0) REVERT: C 154 GLU cc_start: 0.8207 (tt0) cc_final: 0.7949 (tt0) REVERT: C 380 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: C 383 ASP cc_start: 0.8116 (t0) cc_final: 0.7884 (t0) REVERT: D 154 GLU cc_start: 0.8233 (tt0) cc_final: 0.7981 (tt0) REVERT: D 235 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8397 (tmmt) REVERT: D 381 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: E 154 GLU cc_start: 0.8234 (tt0) cc_final: 0.8022 (tt0) REVERT: E 383 ASP cc_start: 0.8171 (t0) cc_final: 0.7962 (t0) REVERT: F 154 GLU cc_start: 0.8180 (tt0) cc_final: 0.7950 (tt0) REVERT: F 235 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7656 (tmmm) REVERT: F 236 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8542 (mm-30) REVERT: F 380 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: F 383 ASP cc_start: 0.8094 (t0) cc_final: 0.7864 (t0) outliers start: 47 outliers final: 24 residues processed: 133 average time/residue: 0.5224 time to fit residues: 77.8721 Evaluate side-chains 115 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 380 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [145, 20, 143, 124, 6, 138, 56, 59, 92, 112, 136] chunk 145 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 141 ASN B 49 GLN B 141 ASN C 49 GLN C 141 ASN D 49 GLN D 141 ASN D 155 HIS E 49 GLN E 141 ASN F 46 GLN F 49 GLN F 141 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.106228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086696 restraints weight = 28007.633| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.59 r_work: 0.3100 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15798 Z= 0.171 Angle : 0.475 5.781 21402 Z= 0.260 Chirality : 0.040 0.141 2358 Planarity : 0.003 0.030 2568 Dihedral : 5.345 47.965 2042 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.18 % Allowed : 17.43 % Favored : 78.39 % 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: 2.59 (0.20), residues: 1782 helix: 2.35 (0.14), residues: 1266 sheet: 1.30 (0.47), residues: 108 loop : -0.19 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 18 TYR 0.020 0.001 TYR D 30 PHE 0.011 0.001 PHE F 41 TRP 0.012 0.001 TRP A 24 HIS 0.003 0.001 HIS F 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (15780) covalent geometry : angle 0.47317 / 0.26 (21366) SS BOND : bond 0.00159 / 0.10 ( 18) SS BOND : angle 1.05271 / 0.68 ( 36) hydrogen bonds : bond 0.03779 / 2.52 ( 1042) hydrogen bonds : angle 4.27764 / 3.09 ( 3081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 93 time to evaluate : 0.630 Fit side-chains REVERT: A 154 GLU cc_start: 0.8214 (tt0) cc_final: 0.7979 (tt0) REVERT: A 235 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8100 (tmmt) REVERT: A 241 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8007 (mtmp) REVERT: A 381 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: B 154 GLU cc_start: 0.8221 (tt0) cc_final: 0.8013 (tt0) REVERT: B 235 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8261 (tmmt) REVERT: B 381 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: B 383 ASP cc_start: 0.8155 (t0) cc_final: 0.7935 (t0) REVERT: C 154 GLU cc_start: 0.8207 (tt0) cc_final: 0.7956 (tt0) REVERT: C 235 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8256 (tmmt) REVERT: D 154 GLU cc_start: 0.8243 (tt0) cc_final: 0.7995 (tt0) REVERT: D 235 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8349 (tmmt) REVERT: D 381 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: D 383 ASP cc_start: 0.8237 (t0) cc_final: 0.7993 (t0) REVERT: E 154 GLU cc_start: 0.8223 (tt0) cc_final: 0.8015 (tt0) REVERT: E 241 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7866 (mtmp) REVERT: F 154 GLU cc_start: 0.8182 (tt0) cc_final: 0.7964 (tt0) REVERT: F 235 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7564 (tmmm) REVERT: F 236 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8711 (mm-30) outliers start: 71 outliers final: 23 residues processed: 152 average time/residue: 0.5154 time to fit residues: 87.9904 Evaluate side-chains 118 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [109, 141, 149, 165, 162, 44, 30, 62, 21, 65, 114] chunk 109 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN A 141 ASN B 49 GLN B 141 ASN C 49 GLN C 141 ASN D 49 GLN D 141 ASN E 49 GLN E 141 ASN F 49 GLN F 141 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.106431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.087064 restraints weight = 27974.073| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.59 r_work: 0.3107 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15798 Z= 0.147 Angle : 0.455 5.687 21402 Z= 0.250 Chirality : 0.039 0.137 2358 Planarity : 0.003 0.029 2568 Dihedral : 5.333 47.876 2042 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.12 % Allowed : 17.79 % Favored : 78.09 % 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: 2.35 (0.20), residues: 1782 helix: 2.18 (0.14), residues: 1302 sheet: 1.07 (0.46), residues: 108 loop : -0.53 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 117 TYR 0.018 0.001 TYR C 281 PHE 0.009 0.001 PHE D 275 TRP 0.012 0.001 TRP A 24 HIS 0.002 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (15780) covalent geometry : angle 0.45335 / 0.25 (21366) SS BOND : bond 0.00140 / 0.09 ( 18) SS BOND : angle 0.97260 / 0.63 ( 36) hydrogen bonds : bond 0.03506 / 2.33 ( 1042) hydrogen bonds : angle 4.11904 / 2.97 ( 3081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 88 time to evaluate : 0.493 Fit side-chains REVERT: A 154 GLU cc_start: 0.8214 (tt0) cc_final: 0.7975 (tt0) REVERT: A 235 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8069 (tmmt) REVERT: B 141 ASN cc_start: 0.8871 (m-40) cc_final: 0.8665 (m110) REVERT: B 154 GLU cc_start: 0.8208 (tt0) cc_final: 0.7987 (tt0) REVERT: B 235 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8222 (tmmt) REVERT: B 381 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: C 154 GLU cc_start: 0.8169 (tt0) cc_final: 0.7926 (tt0) REVERT: C 235 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8235 (tmmt) REVERT: D 154 GLU cc_start: 0.8228 (tt0) cc_final: 0.7983 (tt0) REVERT: D 235 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8297 (tmmt) REVERT: D 383 ASP cc_start: 0.8206 (t0) cc_final: 0.7988 (t0) REVERT: E 154 GLU cc_start: 0.8178 (tt0) cc_final: 0.7956 (tt0) REVERT: E 241 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7924 (mtmp) REVERT: E 381 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: F 154 GLU cc_start: 0.8173 (tt0) cc_final: 0.7958 (tt0) REVERT: F 235 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7725 (tmmm) REVERT: F 236 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8855 (mm-30) REVERT: F 241 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7909 (mtmp) outliers start: 70 outliers final: 23 residues processed: 149 average time/residue: 0.5669 time to fit residues: 93.6856 Evaluate side-chains 117 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [121, 19, 33, 127, 13, 73, 0, 165, 133, 24, 178] chunk 121 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN C 141 ASN D 49 GLN D 141 ASN E 49 GLN F 141 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087514 restraints weight = 28006.805| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.58 r_work: 0.3116 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15798 Z= 0.129 Angle : 0.441 5.615 21402 Z= 0.243 Chirality : 0.039 0.134 2358 Planarity : 0.003 0.028 2568 Dihedral : 5.310 47.787 2042 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.89 % Allowed : 18.37 % Favored : 77.74 % 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: 2.41 (0.20), residues: 1782 helix: 2.22 (0.14), residues: 1302 sheet: 1.06 (0.45), residues: 108 loop : -0.52 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 117 TYR 0.017 0.001 TYR C 281 PHE 0.009 0.001 PHE D 275 TRP 0.012 0.001 TRP A 24 HIS 0.002 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (15780) covalent geometry : angle 0.44016 / 0.24 (21366) SS BOND : bond 0.00112 / 0.07 ( 18) SS BOND : angle 0.86449 / 0.57 ( 36) hydrogen bonds : bond 0.03375 / 2.24 ( 1042) hydrogen bonds : angle 4.04066 / 2.91 ( 3081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 88 time to evaluate : 0.625 Fit side-chains REVERT: A 154 GLU cc_start: 0.8370 (tt0) cc_final: 0.8128 (tt0) REVERT: A 235 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8092 (tmmt) REVERT: A 381 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: B 154 GLU cc_start: 0.8383 (tt0) cc_final: 0.8167 (tt0) REVERT: B 235 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8219 (tmmt) REVERT: C 154 GLU cc_start: 0.8314 (tt0) cc_final: 0.8077 (tt0) REVERT: C 235 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8243 (tmmt) REVERT: C 381 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7636 (mp10) REVERT: D 154 GLU cc_start: 0.8387 (tt0) cc_final: 0.8146 (tt0) REVERT: D 235 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8278 (tmmt) REVERT: D 381 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: D 383 ASP cc_start: 0.8337 (t0) cc_final: 0.8079 (t0) REVERT: E 154 GLU cc_start: 0.8324 (tt0) cc_final: 0.8105 (tt0) REVERT: E 241 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7931 (mtmp) REVERT: F 154 GLU cc_start: 0.8324 (tt0) cc_final: 0.8112 (tt0) REVERT: F 235 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7795 (tmmt) REVERT: F 236 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8871 (mm-30) REVERT: F 241 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7958 (mtmp) REVERT: F 381 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7656 (mp10) outliers start: 66 outliers final: 28 residues processed: 142 average time/residue: 0.5333 time to fit residues: 84.8129 Evaluate side-chains 118 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 79 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 381 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [74, 149, 122, 47, 45, 37, 83, 134, 69, 24, 99] chunk 74 optimal weight: 7.9990 chunk 149 optimal weight: 0.0370 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN C 141 ASN D 49 GLN D 141 ASN E 49 GLN F 49 GLN F 141 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.107492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088130 restraints weight = 27856.752| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.58 r_work: 0.3132 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15798 Z= 0.108 Angle : 0.423 5.463 21402 Z= 0.233 Chirality : 0.038 0.130 2358 Planarity : 0.003 0.029 2568 Dihedral : 5.167 47.428 2040 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.89 % Allowed : 18.49 % Favored : 77.62 % 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: 2.47 (0.20), residues: 1782 helix: 2.27 (0.14), residues: 1302 sheet: 1.25 (0.45), residues: 108 loop : -0.55 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 18 TYR 0.020 0.001 TYR C 281 PHE 0.008 0.001 PHE E 275 TRP 0.012 0.001 TRP D 168 HIS 0.002 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15780) covalent geometry : angle 0.42199 / 0.23 (21366) SS BOND : bond 0.00091 / 0.05 ( 18) SS BOND : angle 0.75289 / 0.50 ( 36) hydrogen bonds : bond 0.03202 / 2.11 ( 1042) hydrogen bonds : angle 3.94875 / 2.84 ( 3081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 86 time to evaluate : 0.633 Fit side-chains REVERT: A 154 GLU cc_start: 0.8199 (tt0) cc_final: 0.7967 (tt0) REVERT: A 235 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8029 (tmmt) REVERT: A 381 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: B 154 GLU cc_start: 0.8203 (tt0) cc_final: 0.7985 (tt0) REVERT: B 235 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8154 (tmmt) REVERT: C 154 GLU cc_start: 0.8152 (tt0) cc_final: 0.7915 (tt0) REVERT: C 235 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8188 (tmmt) REVERT: C 381 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: D 154 GLU cc_start: 0.8186 (tt0) cc_final: 0.7944 (tt0) REVERT: D 235 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8205 (tmmt) REVERT: D 381 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: D 383 ASP cc_start: 0.8194 (t0) cc_final: 0.7984 (t0) REVERT: E 154 GLU cc_start: 0.8171 (tt0) cc_final: 0.7949 (tt0) REVERT: E 241 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7881 (mttp) REVERT: E 381 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7724 (mp10) REVERT: F 154 GLU cc_start: 0.8138 (tt0) cc_final: 0.7931 (tt0) REVERT: F 235 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7704 (tmmt) REVERT: F 236 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8854 (mm-30) REVERT: F 241 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7839 (mttp) REVERT: F 381 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7627 (mp10) outliers start: 66 outliers final: 26 residues processed: 141 average time/residue: 0.5387 time to fit residues: 84.8143 Evaluate side-chains 116 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 381 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [34, 178, 127, 165, 63, 65, 0, 9, 132, 47, 83] chunk 34 optimal weight: 2.9990 chunk 178 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN C 141 ASN D 49 GLN D 141 ASN E 49 GLN F 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087647 restraints weight = 27822.913| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.57 r_work: 0.3123 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15798 Z= 0.120 Angle : 0.433 5.448 21402 Z= 0.237 Chirality : 0.039 0.133 2358 Planarity : 0.003 0.028 2568 Dihedral : 5.176 47.331 2040 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.95 % Allowed : 18.55 % Favored : 77.50 % 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: 2.45 (0.20), residues: 1782 helix: 2.26 (0.14), residues: 1302 sheet: 1.25 (0.46), residues: 108 loop : -0.60 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 117 TYR 0.022 0.001 TYR F 281 PHE 0.008 0.001 PHE D 275 TRP 0.014 0.001 TRP F 168 HIS 0.002 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (15780) covalent geometry : angle 0.43220 / 0.24 (21366) SS BOND : bond 0.00097 / 0.06 ( 18) SS BOND : angle 0.79880 / 0.53 ( 36) hydrogen bonds : bond 0.03270 / 2.16 ( 1042) hydrogen bonds : angle 3.95589 / 2.85 ( 3081) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 78 time to evaluate : 0.612 Fit side-chains REVERT: A 154 GLU cc_start: 0.8207 (tt0) cc_final: 0.7978 (tt0) REVERT: A 235 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8023 (tmmt) REVERT: A 381 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: B 154 GLU cc_start: 0.8215 (tt0) cc_final: 0.7995 (tt0) REVERT: B 235 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8152 (tmmt) REVERT: C 154 GLU cc_start: 0.8159 (tt0) cc_final: 0.7920 (tt0) REVERT: C 235 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8173 (tmmt) REVERT: C 381 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: D 154 GLU cc_start: 0.8177 (tt0) cc_final: 0.7942 (tt0) REVERT: D 235 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8183 (tmmt) REVERT: D 381 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: D 383 ASP cc_start: 0.8212 (t0) cc_final: 0.7992 (t0) REVERT: E 154 GLU cc_start: 0.8172 (tt0) cc_final: 0.7956 (tt0) REVERT: E 241 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7874 (mttp) REVERT: E 381 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: F 154 GLU cc_start: 0.8142 (tt0) cc_final: 0.7934 (tt0) REVERT: F 235 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7707 (tmmt) REVERT: F 236 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8808 (mm-30) REVERT: F 381 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7585 (mp10) outliers start: 67 outliers final: 28 residues processed: 136 average time/residue: 0.5561 time to fit residues: 84.3397 Evaluate side-chains 114 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 381 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [57, 114, 71, 53, 162, 138, 111, 135, 106, 116, 171] chunk 57 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN C 141 ASN D 49 GLN D 141 ASN E 49 GLN F 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087996 restraints weight = 27935.603| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.57 r_work: 0.3129 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15798 Z= 0.112 Angle : 0.428 5.284 21402 Z= 0.235 Chirality : 0.038 0.131 2358 Planarity : 0.003 0.028 2568 Dihedral : 5.164 47.382 2040 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.18 % Allowed : 19.38 % Favored : 77.44 % 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: 2.47 (0.20), residues: 1782 helix: 2.28 (0.14), residues: 1302 sheet: 1.26 (0.45), residues: 108 loop : -0.62 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 117 TYR 0.022 0.001 TYR C 281 PHE 0.010 0.001 PHE C 390 TRP 0.012 0.001 TRP A 24 HIS 0.002 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (15780) covalent geometry : angle 0.42757 / 0.23 (21366) SS BOND : bond 0.00090 / 0.05 ( 18) SS BOND : angle 0.74632 / 0.49 ( 36) hydrogen bonds : bond 0.03216 / 2.13 ( 1042) hydrogen bonds : angle 3.92660 / 2.83 ( 3081) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 79 time to evaluate : 0.478 Fit side-chains REVERT: A 154 GLU cc_start: 0.8208 (tt0) cc_final: 0.7963 (tt0) REVERT: A 235 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8028 (tmmt) REVERT: A 381 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: B 154 GLU cc_start: 0.8224 (tt0) cc_final: 0.8006 (tt0) REVERT: B 235 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8143 (tmmt) REVERT: B 381 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: C 154 GLU cc_start: 0.8151 (tt0) cc_final: 0.7912 (tt0) REVERT: C 235 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8172 (tmmt) REVERT: C 381 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: D 154 GLU cc_start: 0.8173 (tt0) cc_final: 0.7939 (tt0) REVERT: D 235 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8162 (tmmt) REVERT: D 352 SER cc_start: 0.8557 (m) cc_final: 0.8238 (t) REVERT: D 381 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: E 154 GLU cc_start: 0.8183 (tt0) cc_final: 0.7961 (tt0) REVERT: E 381 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: F 154 GLU cc_start: 0.8163 (tt0) cc_final: 0.7956 (tt0) REVERT: F 235 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7680 (tmmt) REVERT: F 236 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8787 (mm-30) REVERT: F 381 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7588 (mp10) outliers start: 54 outliers final: 26 residues processed: 126 average time/residue: 0.5837 time to fit residues: 81.6549 Evaluate side-chains 113 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 381 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [158, 121, 119, 124, 173, 63, 26, 100, 27, 147, 92] chunk 158 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN C 141 ASN D 49 GLN D 141 ASN E 49 GLN F 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.107971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088737 restraints weight = 27785.723| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.57 r_work: 0.3142 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15798 Z= 0.101 Angle : 0.424 6.477 21402 Z= 0.232 Chirality : 0.038 0.128 2358 Planarity : 0.003 0.028 2568 Dihedral : 5.125 47.303 2040 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.89 % Allowed : 19.73 % Favored : 77.39 % 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: 2.51 (0.20), residues: 1782 helix: 2.31 (0.14), residues: 1302 sheet: 1.34 (0.45), residues: 108 loop : -0.61 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 357 TYR 0.021 0.001 TYR C 281 PHE 0.011 0.001 PHE D 390 TRP 0.012 0.001 TRP E 24 HIS 0.002 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (15780) covalent geometry : angle 0.42335 / 0.23 (21366) SS BOND : bond 0.00087 / 0.05 ( 18) SS BOND : angle 0.67614 / 0.45 ( 36) hydrogen bonds : bond 0.03116 / 2.05 ( 1042) hydrogen bonds : angle 3.89526 / 2.80 ( 3081) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 82 time to evaluate : 0.479 Fit side-chains REVERT: A 154 GLU cc_start: 0.8203 (tt0) cc_final: 0.7959 (tt0) REVERT: A 235 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8004 (tmmt) REVERT: A 381 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: B 154 GLU cc_start: 0.8204 (tt0) cc_final: 0.7991 (tt0) REVERT: B 235 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8169 (tmmt) REVERT: B 381 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: C 154 GLU cc_start: 0.8141 (tt0) cc_final: 0.7907 (tt0) REVERT: C 235 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8166 (tmmt) REVERT: C 344 LEU cc_start: 0.8492 (mm) cc_final: 0.8292 (mt) REVERT: C 381 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: D 154 GLU cc_start: 0.8160 (tt0) cc_final: 0.7926 (tt0) REVERT: D 235 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8135 (tmmt) REVERT: D 352 SER cc_start: 0.8571 (m) cc_final: 0.8285 (t) REVERT: D 381 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: E 154 GLU cc_start: 0.8164 (tt0) cc_final: 0.7940 (tt0) REVERT: E 241 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7875 (mttp) REVERT: E 352 SER cc_start: 0.8663 (m) cc_final: 0.8325 (t) REVERT: E 381 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: F 154 GLU cc_start: 0.8146 (tt0) cc_final: 0.7940 (tt0) REVERT: F 235 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7677 (tmmt) REVERT: F 236 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8774 (mm-30) outliers start: 49 outliers final: 22 residues processed: 127 average time/residue: 0.5779 time to fit residues: 81.4471 Evaluate side-chains 112 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [144, 26, 33, 11, 50, 125, 35, 135, 116, 38, 62] chunk 144 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN C 141 ASN D 49 GLN D 141 ASN F 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087835 restraints weight = 27875.299| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.58 r_work: 0.3124 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15798 Z= 0.120 Angle : 0.443 5.786 21402 Z= 0.243 Chirality : 0.039 0.134 2358 Planarity : 0.003 0.028 2568 Dihedral : 5.155 47.315 2040 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.53 % Allowed : 20.20 % Favored : 77.27 % 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: 2.47 (0.20), residues: 1782 helix: 2.27 (0.14), residues: 1302 sheet: 1.27 (0.45), residues: 108 loop : -0.60 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 345 TYR 0.023 0.001 TYR C 281 PHE 0.012 0.001 PHE F 390 TRP 0.012 0.001 TRP D 168 HIS 0.003 0.001 HIS D 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (15780) covalent geometry : angle 0.44267 / 0.24 (21366) SS BOND : bond 0.00095 / 0.06 ( 18) SS BOND : angle 0.75715 / 0.50 ( 36) hydrogen bonds : bond 0.03246 / 2.14 ( 1042) hydrogen bonds : angle 3.95446 / 2.84 ( 3081) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.501 Fit side-chains REVERT: A 154 GLU cc_start: 0.8210 (tt0) cc_final: 0.7967 (tt0) REVERT: A 235 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8006 (tmmt) REVERT: A 381 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: B 154 GLU cc_start: 0.8215 (tt0) cc_final: 0.8001 (tt0) REVERT: B 235 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8113 (tmmt) REVERT: B 381 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: C 154 GLU cc_start: 0.8143 (tt0) cc_final: 0.7910 (tt0) REVERT: C 235 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8165 (tmmt) REVERT: C 352 SER cc_start: 0.8631 (m) cc_final: 0.8340 (t) REVERT: C 381 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: D 154 GLU cc_start: 0.8169 (tt0) cc_final: 0.7937 (tt0) REVERT: D 235 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8139 (tmmt) REVERT: D 352 SER cc_start: 0.8565 (m) cc_final: 0.8297 (t) REVERT: D 381 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: E 154 GLU cc_start: 0.8167 (tt0) cc_final: 0.7941 (tt0) REVERT: E 241 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7882 (mttp) REVERT: E 352 SER cc_start: 0.8686 (m) cc_final: 0.8399 (t) REVERT: E 381 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: F 154 GLU cc_start: 0.8156 (tt0) cc_final: 0.7947 (tt0) REVERT: F 235 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7687 (tmmt) REVERT: F 236 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8764 (mm-30) REVERT: F 344 LEU cc_start: 0.8735 (mm) cc_final: 0.8533 (mp) outliers start: 43 outliers final: 25 residues processed: 118 average time/residue: 0.5963 time to fit residues: 78.0047 Evaluate side-chains 115 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 381 GLN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 GLN Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 235 LYS Chi-restraints excluded: chain F residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [15, 94, 35, 125, 33, 152, 166, 148, 164, 100, 60] chunk 15 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN B 49 GLN C 49 GLN C 141 ASN D 49 GLN D 141 ASN F 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.106451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087128 restraints weight = 27636.324| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.56 r_work: 0.3114 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15798 Z= 0.131 Angle : 0.452 5.724 21402 Z= 0.247 Chirality : 0.039 0.135 2358 Planarity : 0.003 0.028 2568 Dihedral : 5.206 47.912 2040 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.71 % Allowed : 19.96 % Favored : 77.33 % 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: 2.41 (0.20), residues: 1782 helix: 2.23 (0.14), residues: 1302 sheet: 1.17 (0.45), residues: 108 loop : -0.59 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 345 TYR 0.022 0.001 TYR C 281 PHE 0.009 0.001 PHE F 390 TRP 0.013 0.001 TRP D 168 HIS 0.002 0.001 HIS F 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (15780) covalent geometry : angle 0.45099 / 0.25 (21366) SS BOND : bond 0.00104 / 0.07 ( 18) SS BOND : angle 0.80798 / 0.54 ( 36) hydrogen bonds : bond 0.03344 / 2.21 ( 1042) hydrogen bonds : angle 3.99148 / 2.87 ( 3081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.67 seconds wall clock time: 73 minutes 27.41 seconds (4407.41 seconds total)