Starting phenix.real_space_refine on Thu Jul 31 13:25:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io3_35606/07_2025/8io3_35606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io3_35606/07_2025/8io3_35606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8io3_35606/07_2025/8io3_35606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io3_35606/07_2025/8io3_35606.map" model { file = "/net/cci-nas-00/data/ceres_data/8io3_35606/07_2025/8io3_35606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io3_35606/07_2025/8io3_35606.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.009 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 92 5.16 5 C 8972 2.51 5 N 2264 2.21 5 O 2292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13620 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3370 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 16, 'TRANS': 415} Chain breaks: 6 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 9, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'VXI': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 8.32, per 1000 atoms: 0.61 Number of scatterers: 13620 At special positions: 0 Unit cell: (122.558, 122.558, 112.038, 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 92 16.00 O 2292 8.00 N 2264 7.00 C 8972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 72.7% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'C' and resid 50 through 54 removed outlier: 4.095A pdb=" N LEU C 53 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 67 through 81 removed outlier: 3.697A pdb=" N VAL C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 117 removed outlier: 3.771A pdb=" N PHE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 123 through 145 removed outlier: 3.879A pdb=" N LEU C 141 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 172 removed outlier: 3.505A pdb=" N THR C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 removed outlier: 3.724A pdb=" N ILE C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 191 removed outlier: 4.044A pdb=" N ILE C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 219 through 222 removed outlier: 3.615A pdb=" N LEU C 222 " --> pdb=" O LEU C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 222' Processing helix chain 'C' and resid 223 through 238 removed outlier: 3.702A pdb=" N ARG C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 276 removed outlier: 3.719A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Proline residue: C 273 - end of helix removed outlier: 3.897A pdb=" N GLN C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 293 through 310 Processing helix chain 'C' and resid 321 through 351 removed outlier: 3.602A pdb=" N TRP C 326 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 355 through 375 removed outlier: 3.915A pdb=" N TYR C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 361 " --> pdb=" O ARG C 357 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS C 374 " --> pdb=" O TYR C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 393 Processing helix chain 'C' and resid 398 through 406 removed outlier: 3.537A pdb=" N LEU C 403 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 419 Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.763A pdb=" N PHE C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 54 removed outlier: 4.095A pdb=" N LEU A 53 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.697A pdb=" N VAL A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 117 removed outlier: 3.771A pdb=" N PHE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 123 through 145 removed outlier: 3.879A pdb=" N LEU A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.505A pdb=" N THR A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.724A pdb=" N ILE A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 removed outlier: 4.044A pdb=" N ILE A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 219 through 222 removed outlier: 3.615A pdb=" N LEU A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 222' Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.702A pdb=" N ARG A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 276 removed outlier: 3.719A pdb=" N VAL A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 267 " --> pdb=" O HIS A 263 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.897A pdb=" N GLN A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 293 through 310 Processing helix chain 'A' and resid 321 through 351 removed outlier: 3.602A pdb=" N TRP A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 355 through 375 removed outlier: 3.915A pdb=" N TYR A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 393 Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.537A pdb=" N LEU A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 419 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 518 through 528 removed outlier: 3.763A pdb=" N PHE A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 4.095A pdb=" N LEU B 53 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 67 through 81 removed outlier: 3.697A pdb=" N VAL B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 117 removed outlier: 3.771A pdb=" N PHE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 123 through 145 removed outlier: 3.879A pdb=" N LEU B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.505A pdb=" N THR B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 3.724A pdb=" N ILE B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 191 removed outlier: 4.044A pdb=" N ILE B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 219 through 222 removed outlier: 3.615A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 223 through 238 removed outlier: 3.702A pdb=" N ARG B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 276 removed outlier: 3.719A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) Proline residue: B 273 - end of helix removed outlier: 3.897A pdb=" N GLN B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 293 through 310 Processing helix chain 'B' and resid 321 through 351 removed outlier: 3.602A pdb=" N TRP B 326 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 355 through 375 removed outlier: 3.915A pdb=" N TYR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 374 " --> pdb=" O TYR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 393 Processing helix chain 'B' and resid 398 through 406 removed outlier: 3.537A pdb=" N LEU B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 419 Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 518 through 528 removed outlier: 3.763A pdb=" N PHE B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.094A pdb=" N LEU D 53 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.696A pdb=" N VAL D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 117 removed outlier: 3.771A pdb=" N PHE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Proline residue: D 112 - end of helix Processing helix chain 'D' and resid 123 through 145 removed outlier: 3.880A pdb=" N LEU D 141 " --> pdb=" O PHE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.505A pdb=" N THR D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.725A pdb=" N ILE D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 removed outlier: 4.044A pdb=" N ILE D 186 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 219 through 222 removed outlier: 3.615A pdb=" N LEU D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 222' Processing helix chain 'D' and resid 223 through 238 removed outlier: 3.702A pdb=" N ARG D 229 " --> pdb=" O SER D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 276 removed outlier: 3.720A pdb=" N VAL D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS D 267 " --> pdb=" O HIS D 263 " (cutoff:3.500A) Proline residue: D 273 - end of helix removed outlier: 3.897A pdb=" N GLN D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 293 through 310 Processing helix chain 'D' and resid 321 through 351 removed outlier: 3.602A pdb=" N TRP D 326 " --> pdb=" O MET D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 355 through 375 removed outlier: 3.915A pdb=" N TYR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN D 361 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS D 374 " --> pdb=" O TYR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 393 Processing helix chain 'D' and resid 398 through 406 removed outlier: 3.537A pdb=" N LEU D 403 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 419 Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 518 through 528 removed outlier: 3.763A pdb=" N PHE D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 445 through 448 Processing sheet with id=AA2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 448 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 448 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'D' and resid 445 through 448 Processing sheet with id=AA8, first strand: chain 'D' and resid 473 through 474 840 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2036 1.27 - 1.41: 3966 1.41 - 1.56: 7818 1.56 - 1.70: 8 1.70 - 1.85: 164 Bond restraints: 13992 Sorted by residual: bond pdb=" CAT VXI D 801 " pdb=" CAU VXI D 801 " ideal model delta sigma weight residual 1.394 1.787 -0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" CAT VXI A 801 " pdb=" CAU VXI A 801 " ideal model delta sigma weight residual 1.394 1.787 -0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" CAT VXI B 801 " pdb=" CAU VXI B 801 " ideal model delta sigma weight residual 1.394 1.787 -0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" CAT VXI C 801 " pdb=" CAU VXI C 801 " ideal model delta sigma weight residual 1.394 1.787 -0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" CAR VXI C 801 " pdb=" CAT VXI C 801 " ideal model delta sigma weight residual 1.512 1.845 -0.333 2.00e-02 2.50e+03 2.77e+02 ... (remaining 13987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 18375 2.19 - 4.38: 501 4.38 - 6.57: 84 6.57 - 8.75: 52 8.75 - 10.94: 24 Bond angle restraints: 19036 Sorted by residual: angle pdb=" C LEU D 517 " pdb=" N SER D 518 " pdb=" CA SER D 518 " ideal model delta sigma weight residual 121.31 128.22 -6.91 1.49e+00 4.50e-01 2.15e+01 angle pdb=" C LEU C 517 " pdb=" N SER C 518 " pdb=" CA SER C 518 " ideal model delta sigma weight residual 121.31 128.19 -6.88 1.49e+00 4.50e-01 2.13e+01 angle pdb=" C LEU A 517 " pdb=" N SER A 518 " pdb=" CA SER A 518 " ideal model delta sigma weight residual 121.31 128.19 -6.88 1.49e+00 4.50e-01 2.13e+01 angle pdb=" C LEU B 517 " pdb=" N SER B 518 " pdb=" CA SER B 518 " ideal model delta sigma weight residual 121.31 128.19 -6.88 1.49e+00 4.50e-01 2.13e+01 angle pdb=" C VAL B 455 " pdb=" N VAL B 456 " pdb=" CA VAL B 456 " ideal model delta sigma weight residual 121.97 130.08 -8.11 1.80e+00 3.09e-01 2.03e+01 ... (remaining 19031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 7730 14.77 - 29.54: 330 29.54 - 44.30: 44 44.30 - 59.07: 12 59.07 - 73.84: 16 Dihedral angle restraints: 8132 sinusoidal: 3076 harmonic: 5056 Sorted by residual: dihedral pdb=" CA VAL B 455 " pdb=" C VAL B 455 " pdb=" N VAL B 456 " pdb=" CA VAL B 456 " ideal model delta harmonic sigma weight residual 180.00 135.73 44.27 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CA VAL A 455 " pdb=" C VAL A 455 " pdb=" N VAL A 456 " pdb=" CA VAL A 456 " ideal model delta harmonic sigma weight residual 180.00 135.73 44.27 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CA VAL C 455 " pdb=" C VAL C 455 " pdb=" N VAL C 456 " pdb=" CA VAL C 456 " ideal model delta harmonic sigma weight residual 180.00 135.73 44.27 0 5.00e+00 4.00e-02 7.84e+01 ... (remaining 8129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1250 0.039 - 0.079: 667 0.079 - 0.118: 187 0.118 - 0.157: 17 0.157 - 0.196: 35 Chirality restraints: 2156 Sorted by residual: chirality pdb=" CG LEU D 410 " pdb=" CB LEU D 410 " pdb=" CD1 LEU D 410 " pdb=" CD2 LEU D 410 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CG LEU A 410 " pdb=" CB LEU A 410 " pdb=" CD1 LEU A 410 " pdb=" CD2 LEU A 410 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" CG LEU B 410 " pdb=" CB LEU B 410 " pdb=" CD1 LEU B 410 " pdb=" CD2 LEU B 410 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 2153 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 455 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C VAL D 455 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL D 455 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL D 456 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 455 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C VAL A 455 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 455 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL A 456 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 455 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C VAL C 455 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL C 455 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL C 456 " -0.015 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 4610 2.88 - 3.38: 12743 3.38 - 3.89: 21519 3.89 - 4.39: 22667 4.39 - 4.90: 40154 Nonbonded interactions: 101693 Sorted by model distance: nonbonded pdb=" OE1 GLN B 359 " pdb=" NE2 GLN D 366 " model vdw 2.369 3.120 nonbonded pdb=" OE1 GLN C 359 " pdb=" NE2 GLN A 366 " model vdw 2.397 3.120 nonbonded pdb=" OE1 GLN A 359 " pdb=" NE2 GLN B 366 " model vdw 2.397 3.120 nonbonded pdb=" NE2 GLN C 366 " pdb=" OE1 GLN D 359 " model vdw 2.398 3.120 nonbonded pdb=" OE2 GLU C 458 " pdb=" N SER C 505 " model vdw 2.415 3.120 ... (remaining 101688 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.850 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.010 Find NCS groups from input model: 0.260 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.015 0.393 13992 Z= 0.726 Angle : 1.000 10.942 19036 Z= 0.535 Chirality : 0.052 0.196 2156 Planarity : 0.006 0.044 2340 Dihedral : 9.714 73.839 4852 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.58 % Allowed : 0.58 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.16), residues: 1672 helix: -1.33 (0.12), residues: 1128 sheet: -0.61 (0.67), residues: 72 loop : -3.00 (0.23), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 234 HIS 0.015 0.003 HIS B 239 PHE 0.015 0.002 PHE D 449 TYR 0.028 0.002 TYR D 511 ARG 0.004 0.001 ARG D 229 Details of bonding type rmsd hydrogen bonds : bond 0.15619 ( 840) hydrogen bonds : angle 6.04194 ( 2484) covalent geometry : bond 0.01470 (13992) covalent geometry : angle 0.99961 (19036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.561 Fit side-chains REVERT: C 523 ASN cc_start: 0.9378 (m-40) cc_final: 0.9175 (m-40) REVERT: A 523 ASN cc_start: 0.9377 (m-40) cc_final: 0.9173 (m-40) REVERT: B 523 ASN cc_start: 0.9377 (m-40) cc_final: 0.9176 (m-40) REVERT: D 523 ASN cc_start: 0.9388 (m-40) cc_final: 0.9182 (m-40) outliers start: 8 outliers final: 8 residues processed: 132 average time/residue: 0.3137 time to fit residues: 58.1366 Evaluate side-chains 87 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 456 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 50.0000 chunk 100 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN C 292 HIS C 300 HIS C 308 HIS C 470 HIS A 107 ASN A 292 HIS A 300 HIS A 308 HIS A 470 HIS B 107 ASN B 292 HIS B 300 HIS B 308 HIS B 470 HIS D 292 HIS D 300 HIS D 308 HIS D 470 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.069261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052883 restraints weight = 57424.338| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.36 r_work: 0.2921 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13992 Z= 0.155 Angle : 0.570 6.952 19036 Z= 0.301 Chirality : 0.041 0.119 2156 Planarity : 0.004 0.039 2340 Dihedral : 6.737 57.628 2004 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.02 % Allowed : 3.06 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1672 helix: 1.25 (0.15), residues: 1148 sheet: 0.87 (0.65), residues: 72 loop : -2.34 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 234 HIS 0.006 0.001 HIS D 308 PHE 0.010 0.001 PHE D 467 TYR 0.015 0.001 TYR B 511 ARG 0.002 0.000 ARG A 507 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 840) hydrogen bonds : angle 4.12064 ( 2484) covalent geometry : bond 0.00358 (13992) covalent geometry : angle 0.56979 (19036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 2.182 Fit side-chains REVERT: C 523 ASN cc_start: 0.9400 (m-40) cc_final: 0.9193 (m-40) REVERT: A 523 ASN cc_start: 0.9402 (m-40) cc_final: 0.9196 (m-40) REVERT: B 523 ASN cc_start: 0.9401 (m-40) cc_final: 0.9197 (m-40) REVERT: D 523 ASN cc_start: 0.9404 (m-40) cc_final: 0.9195 (m-40) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 0.2944 time to fit residues: 48.2151 Evaluate side-chains 91 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain D residue 425 HIS Chi-restraints excluded: chain D residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 123 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 168 optimal weight: 30.0000 chunk 161 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.068926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052474 restraints weight = 57281.976| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.34 r_work: 0.2904 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13992 Z= 0.149 Angle : 0.529 6.758 19036 Z= 0.276 Chirality : 0.041 0.120 2156 Planarity : 0.003 0.040 2340 Dihedral : 6.318 55.789 2000 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.68 % Allowed : 3.35 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1672 helix: 2.12 (0.16), residues: 1156 sheet: 1.43 (0.66), residues: 72 loop : -1.89 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 326 HIS 0.005 0.001 HIS D 308 PHE 0.010 0.001 PHE B 417 TYR 0.016 0.001 TYR B 511 ARG 0.002 0.000 ARG B 226 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 840) hydrogen bonds : angle 3.81265 ( 2484) covalent geometry : bond 0.00346 (13992) covalent geometry : angle 0.52900 (19036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 2.078 Fit side-chains REVERT: C 309 MET cc_start: 0.9266 (mmm) cc_final: 0.9041 (mmm) REVERT: C 523 ASN cc_start: 0.9397 (m-40) cc_final: 0.9184 (m-40) REVERT: A 309 MET cc_start: 0.9268 (mmm) cc_final: 0.9044 (mmm) REVERT: A 523 ASN cc_start: 0.9398 (m-40) cc_final: 0.9186 (m-40) REVERT: B 309 MET cc_start: 0.9276 (mmm) cc_final: 0.9052 (mmm) REVERT: B 523 ASN cc_start: 0.9401 (m-40) cc_final: 0.9189 (m-40) REVERT: D 309 MET cc_start: 0.9260 (mmm) cc_final: 0.9038 (mmm) REVERT: D 523 ASN cc_start: 0.9399 (m-40) cc_final: 0.9186 (m-40) outliers start: 23 outliers final: 13 residues processed: 99 average time/residue: 0.3275 time to fit residues: 52.7064 Evaluate side-chains 89 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 425 HIS Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.069579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052940 restraints weight = 57326.938| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.34 r_work: 0.2915 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13992 Z= 0.122 Angle : 0.490 6.636 19036 Z= 0.256 Chirality : 0.040 0.119 2156 Planarity : 0.003 0.041 2340 Dihedral : 6.201 57.663 2000 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.46 % Allowed : 4.52 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.22), residues: 1672 helix: 2.53 (0.16), residues: 1152 sheet: 1.33 (0.82), residues: 52 loop : -1.44 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.004 0.001 HIS D 308 PHE 0.009 0.001 PHE D 270 TYR 0.014 0.001 TYR D 511 ARG 0.003 0.000 ARG B 226 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 840) hydrogen bonds : angle 3.60979 ( 2484) covalent geometry : bond 0.00281 (13992) covalent geometry : angle 0.48977 (19036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 2.324 Fit side-chains REVERT: C 523 ASN cc_start: 0.9395 (m-40) cc_final: 0.9180 (m110) REVERT: A 523 ASN cc_start: 0.9397 (m-40) cc_final: 0.9182 (m110) REVERT: B 523 ASN cc_start: 0.9397 (m-40) cc_final: 0.9183 (m110) REVERT: D 523 ASN cc_start: 0.9400 (m-40) cc_final: 0.9189 (m110) outliers start: 20 outliers final: 15 residues processed: 94 average time/residue: 0.4480 time to fit residues: 68.3347 Evaluate side-chains 92 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain D residue 425 HIS Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 456 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 90 optimal weight: 10.0000 chunk 171 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 40.0000 chunk 147 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 ASN C 269 GLN A 269 GLN B 253 ASN B 269 GLN D 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.069951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053348 restraints weight = 57023.050| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.33 r_work: 0.2919 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13992 Z= 0.106 Angle : 0.472 6.532 19036 Z= 0.246 Chirality : 0.040 0.120 2156 Planarity : 0.003 0.042 2340 Dihedral : 6.154 59.074 2000 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.46 % Allowed : 5.03 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.22), residues: 1672 helix: 2.71 (0.16), residues: 1152 sheet: 1.43 (0.66), residues: 72 loop : -1.41 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.003 0.001 HIS C 390 PHE 0.009 0.001 PHE C 270 TYR 0.012 0.001 TYR C 511 ARG 0.002 0.000 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 840) hydrogen bonds : angle 3.52570 ( 2484) covalent geometry : bond 0.00238 (13992) covalent geometry : angle 0.47232 (19036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.557 Fit side-chains REVERT: C 523 ASN cc_start: 0.9401 (m-40) cc_final: 0.9185 (m110) REVERT: A 523 ASN cc_start: 0.9402 (m-40) cc_final: 0.9185 (m110) REVERT: B 523 ASN cc_start: 0.9406 (m-40) cc_final: 0.9191 (m110) REVERT: D 523 ASN cc_start: 0.9410 (m-40) cc_final: 0.9201 (m110) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.1958 time to fit residues: 30.4849 Evaluate side-chains 88 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 425 HIS Chi-restraints excluded: chain D residue 456 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 30.0000 chunk 113 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 165 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN D 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.067437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050688 restraints weight = 58298.986| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.37 r_work: 0.2846 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13992 Z= 0.209 Angle : 0.568 6.668 19036 Z= 0.296 Chirality : 0.043 0.153 2156 Planarity : 0.003 0.041 2340 Dihedral : 6.317 56.873 2000 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.17 % Allowed : 5.25 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.22), residues: 1672 helix: 2.71 (0.16), residues: 1156 sheet: 1.49 (0.67), residues: 72 loop : -1.17 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS D 308 PHE 0.012 0.002 PHE A 252 TYR 0.016 0.002 TYR D 511 ARG 0.003 0.000 ARG D 229 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 840) hydrogen bonds : angle 3.72171 ( 2484) covalent geometry : bond 0.00497 (13992) covalent geometry : angle 0.56846 (19036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.711 Fit side-chains REVERT: C 523 ASN cc_start: 0.9411 (m-40) cc_final: 0.9190 (m110) REVERT: A 523 ASN cc_start: 0.9412 (m-40) cc_final: 0.9191 (m110) REVERT: B 523 ASN cc_start: 0.9413 (m-40) cc_final: 0.9193 (m110) REVERT: D 523 ASN cc_start: 0.9416 (m-40) cc_final: 0.9192 (m110) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.2067 time to fit residues: 31.2580 Evaluate side-chains 88 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 425 HIS Chi-restraints excluded: chain D residue 456 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 6.9990 chunk 121 optimal weight: 30.0000 chunk 126 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.067247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050500 restraints weight = 57865.952| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.34 r_work: 0.2853 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13992 Z= 0.198 Angle : 0.559 6.852 19036 Z= 0.290 Chirality : 0.043 0.132 2156 Planarity : 0.003 0.042 2340 Dihedral : 6.353 58.802 2000 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.87 % Allowed : 5.47 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.22), residues: 1672 helix: 2.74 (0.15), residues: 1156 sheet: 1.32 (0.66), residues: 72 loop : -1.06 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 234 HIS 0.005 0.001 HIS A 390 PHE 0.010 0.001 PHE A 252 TYR 0.016 0.001 TYR A 511 ARG 0.003 0.000 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 840) hydrogen bonds : angle 3.70950 ( 2484) covalent geometry : bond 0.00470 (13992) covalent geometry : angle 0.55883 (19036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.631 Fit side-chains REVERT: C 523 ASN cc_start: 0.9405 (m-40) cc_final: 0.9175 (m110) REVERT: A 523 ASN cc_start: 0.9408 (m-40) cc_final: 0.9180 (m110) REVERT: B 523 ASN cc_start: 0.9406 (m-40) cc_final: 0.9178 (m110) REVERT: D 523 ASN cc_start: 0.9403 (m-40) cc_final: 0.9176 (m110) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.2105 time to fit residues: 30.6222 Evaluate side-chains 84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 425 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 104 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 21 optimal weight: 0.3980 chunk 13 optimal weight: 7.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.067924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051240 restraints weight = 57539.706| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.33 r_work: 0.2875 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13992 Z= 0.149 Angle : 0.527 6.524 19036 Z= 0.273 Chirality : 0.041 0.143 2156 Planarity : 0.003 0.042 2340 Dihedral : 6.092 59.804 1996 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.58 % Allowed : 5.83 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.22), residues: 1672 helix: 2.85 (0.15), residues: 1156 sheet: 1.31 (0.65), residues: 72 loop : -0.97 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS C 390 PHE 0.009 0.001 PHE D 467 TYR 0.014 0.001 TYR D 511 ARG 0.003 0.000 ARG C 226 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 840) hydrogen bonds : angle 3.60752 ( 2484) covalent geometry : bond 0.00347 (13992) covalent geometry : angle 0.52659 (19036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.711 Fit side-chains REVERT: C 523 ASN cc_start: 0.9398 (m-40) cc_final: 0.9166 (m110) REVERT: A 523 ASN cc_start: 0.9403 (m-40) cc_final: 0.9170 (m110) REVERT: B 523 ASN cc_start: 0.9403 (m-40) cc_final: 0.9173 (m110) REVERT: D 523 ASN cc_start: 0.9399 (m-40) cc_final: 0.9165 (m110) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.2113 time to fit residues: 29.0919 Evaluate side-chains 84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 425 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 10 optimal weight: 0.0470 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 overall best weight: 2.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.069769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053259 restraints weight = 56532.925| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.32 r_work: 0.2915 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13992 Z= 0.097 Angle : 0.482 6.603 19036 Z= 0.250 Chirality : 0.039 0.126 2156 Planarity : 0.003 0.043 2340 Dihedral : 5.764 55.736 1996 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.58 % Allowed : 6.12 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.22), residues: 1672 helix: 2.95 (0.15), residues: 1156 sheet: 1.14 (0.80), residues: 52 loop : -0.81 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 96 HIS 0.004 0.001 HIS A 390 PHE 0.011 0.001 PHE D 467 TYR 0.011 0.001 TYR C 511 ARG 0.002 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 840) hydrogen bonds : angle 3.44336 ( 2484) covalent geometry : bond 0.00211 (13992) covalent geometry : angle 0.48245 (19036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.617 Fit side-chains REVERT: C 523 ASN cc_start: 0.9406 (m-40) cc_final: 0.9179 (m110) REVERT: A 523 ASN cc_start: 0.9408 (m-40) cc_final: 0.9182 (m110) REVERT: B 523 ASN cc_start: 0.9407 (m-40) cc_final: 0.9182 (m110) REVERT: D 523 ASN cc_start: 0.9405 (m-40) cc_final: 0.9178 (m110) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.2234 time to fit residues: 30.4420 Evaluate side-chains 84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 425 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.068083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.051434 restraints weight = 57459.080| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.33 r_work: 0.2881 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13992 Z= 0.155 Angle : 0.549 8.224 19036 Z= 0.283 Chirality : 0.042 0.189 2156 Planarity : 0.003 0.042 2340 Dihedral : 5.943 56.929 1996 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.58 % Allowed : 6.41 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.22), residues: 1672 helix: 2.90 (0.15), residues: 1160 sheet: 1.30 (0.80), residues: 52 loop : -0.79 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS D 390 PHE 0.013 0.001 PHE D 467 TYR 0.014 0.001 TYR D 511 ARG 0.003 0.000 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 840) hydrogen bonds : angle 3.53377 ( 2484) covalent geometry : bond 0.00367 (13992) covalent geometry : angle 0.54864 (19036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3344 Ramachandran restraints generated. 1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.676 Fit side-chains REVERT: C 523 ASN cc_start: 0.9393 (m-40) cc_final: 0.9156 (m110) REVERT: A 523 ASN cc_start: 0.9398 (m-40) cc_final: 0.9162 (m110) REVERT: B 523 ASN cc_start: 0.9398 (m-40) cc_final: 0.9164 (m110) REVERT: D 523 ASN cc_start: 0.9399 (m-40) cc_final: 0.9163 (m110) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.2146 time to fit residues: 29.8340 Evaluate side-chains 84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 425 HIS Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 425 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.068178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051556 restraints weight = 57910.987| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.37 r_work: 0.2883 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13992 Z= 0.150 Angle : 0.538 7.871 19036 Z= 0.280 Chirality : 0.042 0.212 2156 Planarity : 0.003 0.042 2340 Dihedral : 5.926 55.513 1996 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.80 % Allowed : 6.20 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.22), residues: 1672 helix: 2.85 (0.15), residues: 1160 sheet: 1.25 (0.79), residues: 52 loop : -0.78 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 96 HIS 0.005 0.001 HIS C 390 PHE 0.013 0.001 PHE D 467 TYR 0.014 0.001 TYR D 511 ARG 0.004 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 840) hydrogen bonds : angle 3.54492 ( 2484) covalent geometry : bond 0.00350 (13992) covalent geometry : angle 0.53815 (19036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9787.63 seconds wall clock time: 175 minutes 50.61 seconds (10550.61 seconds total)