Starting phenix.real_space_refine on Fri Jul 3 04:32:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lid_23374/07_2026/7lid_23374.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lid_23374/07_2026/7lid_23374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lid_23374/07_2026/7lid_23374.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lid_23374/07_2026/7lid_23374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lid_23374/07_2026/7lid_23374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lid_23374/07_2026/7lid_23374.map" model { file = "/net/cci-nas-00/data/ceres_data/7lid_23374/07_2026/7lid_23374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lid_23374/07_2026/7lid_23374.cif" } resolution = 2.9 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= 0.002 sd= 0.105 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 120 5.16 5 C 7992 2.51 5 N 1936 2.21 5 O 2092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12140 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'EOL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.46, per 1000 atoms: 0.20 Number of scatterers: 12140 At special positions: 0 Unit cell: (112.27, 112.27, 92.7, 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 120 16.00 O 2092 8.00 N 1936 7.00 C 7992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 575.2 milliseconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 82.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 13 through 31 removed outlier: 3.676A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.674A pdb=" N LYS A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 48 through 75 removed outlier: 3.718A pdb=" N CYS A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 73 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 105 removed outlier: 3.657A pdb=" N ALA A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 3.756A pdb=" N THR A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 169 removed outlier: 3.919A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 194 through 247 removed outlier: 4.410A pdb=" N ALA A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.943A pdb=" N GLY A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 366 removed outlier: 4.166A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 407 removed outlier: 3.771A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.867A pdb=" N VAL A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.693A pdb=" N GLN A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 469 removed outlier: 3.677A pdb=" N ILE A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 31 removed outlier: 3.676A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 18 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.674A pdb=" N LYS B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.716A pdb=" N CYS B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 73 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 105 removed outlier: 3.658A pdb=" N ALA B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 removed outlier: 3.757A pdb=" N THR B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 169 removed outlier: 3.919A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 194 through 247 removed outlier: 4.411A pdb=" N ALA B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 3.944A pdb=" N GLY B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 366 removed outlier: 4.166A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 407 removed outlier: 3.771A pdb=" N LEU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.867A pdb=" N VAL B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 433 removed outlier: 3.693A pdb=" N GLN B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 469 removed outlier: 3.676A pdb=" N ILE B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 465 " --> pdb=" O TYR B 461 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 31 removed outlier: 3.676A pdb=" N LEU C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 18 " --> pdb=" O TYR C 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY C 25 " --> pdb=" O ILE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 47 removed outlier: 3.673A pdb=" N LYS C 47 " --> pdb=" O ASN C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 44 through 47' Processing helix chain 'C' and resid 48 through 75 removed outlier: 3.716A pdb=" N CYS C 56 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C 74 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 75 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 105 removed outlier: 3.658A pdb=" N ALA C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 removed outlier: 3.756A pdb=" N THR C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 169 removed outlier: 3.918A pdb=" N SER C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 194 through 247 removed outlier: 4.411A pdb=" N ALA C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.943A pdb=" N GLY C 247 " --> pdb=" O CYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 366 removed outlier: 4.165A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 407 removed outlier: 3.771A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.868A pdb=" N VAL C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 433 removed outlier: 3.692A pdb=" N GLN C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 469 removed outlier: 3.677A pdb=" N ILE C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 464 " --> pdb=" O THR C 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 465 " --> pdb=" O TYR C 461 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 31 removed outlier: 3.677A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 47 removed outlier: 3.674A pdb=" N LYS D 47 " --> pdb=" O ASN D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 44 through 47' Processing helix chain 'D' and resid 48 through 75 removed outlier: 3.716A pdb=" N CYS D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 73 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 105 removed outlier: 3.658A pdb=" N ALA D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 116 removed outlier: 3.756A pdb=" N THR D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 169 removed outlier: 3.918A pdb=" N SER D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 194 through 247 removed outlier: 4.411A pdb=" N ALA D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.944A pdb=" N GLY D 247 " --> pdb=" O CYS D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 366 removed outlier: 4.166A pdb=" N SER D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 407 removed outlier: 3.772A pdb=" N LEU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.867A pdb=" N VAL D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 433 removed outlier: 3.693A pdb=" N GLN D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 469 removed outlier: 3.676A pdb=" N ILE D 463 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 464 " --> pdb=" O THR D 460 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 465 " --> pdb=" O TYR D 461 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2784 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: 1.68 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3354 1.34 - 1.46: 2242 1.46 - 1.57: 6648 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 12416 Sorted by residual: bond pdb=" C8 EOL B 900 " pdb=" C9 EOL B 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C8 EOL A 900 " pdb=" C9 EOL A 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C8 EOL D 900 " pdb=" C9 EOL D 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C8 EOL C 900 " pdb=" C9 EOL C 900 " ideal model delta sigma weight residual 1.328 1.525 -0.197 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C SER D 195 " pdb=" N PRO D 196 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.23e-02 6.61e+03 1.13e+01 ... (remaining 12411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 16486 2.55 - 5.10: 308 5.10 - 7.65: 34 7.65 - 10.20: 8 10.20 - 12.75: 4 Bond angle restraints: 16840 Sorted by residual: angle pdb=" C7 EOL D 900 " pdb=" C8 EOL D 900 " pdb=" C9 EOL D 900 " ideal model delta sigma weight residual 124.74 111.99 12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C7 EOL A 900 " pdb=" C8 EOL A 900 " pdb=" C9 EOL A 900 " ideal model delta sigma weight residual 124.74 112.02 12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C7 EOL C 900 " pdb=" C8 EOL C 900 " pdb=" C9 EOL C 900 " ideal model delta sigma weight residual 124.74 112.05 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C7 EOL B 900 " pdb=" C8 EOL B 900 " pdb=" C9 EOL B 900 " ideal model delta sigma weight residual 124.74 112.05 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" C THR D 194 " pdb=" N SER D 195 " pdb=" CA SER D 195 " ideal model delta sigma weight residual 120.26 125.27 -5.01 1.34e+00 5.57e-01 1.40e+01 ... (remaining 16835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6487 17.99 - 35.98: 610 35.98 - 53.97: 155 53.97 - 71.96: 20 71.96 - 89.96: 4 Dihedral angle restraints: 7276 sinusoidal: 2768 harmonic: 4508 Sorted by residual: dihedral pdb=" CA ILE C 21 " pdb=" C ILE C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta harmonic sigma weight residual 180.00 159.99 20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE D 21 " pdb=" C ILE D 21 " pdb=" N LYS D 22 " pdb=" CA LYS D 22 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE B 21 " pdb=" C ILE B 21 " pdb=" N LYS B 22 " pdb=" CA LYS B 22 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1151 0.032 - 0.064: 593 0.064 - 0.095: 180 0.095 - 0.127: 60 0.127 - 0.159: 32 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CB VAL B 184 " pdb=" CA VAL B 184 " pdb=" CG1 VAL B 184 " pdb=" CG2 VAL B 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB VAL C 184 " pdb=" CA VAL C 184 " pdb=" CG1 VAL C 184 " pdb=" CG2 VAL C 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB VAL D 184 " pdb=" CA VAL D 184 " pdb=" CG1 VAL D 184 " pdb=" CG2 VAL D 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 2013 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 38 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO B 39 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 38 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 39 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 38 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO C 39 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " 0.035 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4077 2.84 - 3.36: 11738 3.36 - 3.87: 20064 3.87 - 4.39: 21392 4.39 - 4.90: 37785 Nonbonded interactions: 95056 Sorted by model distance: nonbonded pdb=" O THR A 348 " pdb=" OG1 THR A 352 " model vdw 2.330 3.040 nonbonded pdb=" O THR C 348 " pdb=" OG1 THR C 352 " model vdw 2.330 3.040 nonbonded pdb=" O THR D 348 " pdb=" OG1 THR D 352 " model vdw 2.330 3.040 nonbonded pdb=" O THR B 348 " pdb=" OG1 THR B 352 " model vdw 2.331 3.040 nonbonded pdb=" OG SER D 78 " pdb=" OE1 GLN D 81 " model vdw 2.388 3.040 ... (remaining 95051 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.780 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.006 0.197 12416 Z= 0.316 Angle : 0.877 12.753 16840 Z= 0.494 Chirality : 0.044 0.159 2016 Planarity : 0.007 0.062 2016 Dihedral : 15.132 89.956 4348 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.47 % Allowed : 5.90 % Favored : 92.63 % 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: -2.01 (0.19), residues: 1500 helix: -0.77 (0.13), residues: 1188 sheet: None (None), residues: 0 loop : -3.07 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 139 TYR 0.023 0.002 TYR A 380 PHE 0.021 0.002 PHE D 363 TRP 0.015 0.002 TRP C 158 HIS 0.003 0.001 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.32 (12416) covalent geometry : angle 0.87722 / 0.49 (16840) hydrogen bonds : bond 0.13201 / 8.94 ( 928) hydrogen bonds : angle 5.04240 / 3.66 ( 2784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.480 Fit side-chains REVERT: A 371 PHE cc_start: 0.7433 (t80) cc_final: 0.7220 (t80) REVERT: B 371 PHE cc_start: 0.7726 (t80) cc_final: 0.7448 (t80) REVERT: C 191 ASP cc_start: 0.7574 (p0) cc_final: 0.7371 (p0) REVERT: D 191 ASP cc_start: 0.7901 (p0) cc_final: 0.7669 (p0) REVERT: D 371 PHE cc_start: 0.7493 (t80) cc_final: 0.7245 (t80) outliers start: 20 outliers final: 9 residues processed: 268 average time/residue: 0.3345 time to fit residues: 101.7330 Evaluate side-chains 165 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN B 52 GLN B 105 ASN B 467 GLN C 52 GLN C 467 GLN D 52 GLN D 105 ASN D 467 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115157 restraints weight = 17745.406| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.37 r_work: 0.3359 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12416 Z= 0.140 Angle : 0.566 6.448 16840 Z= 0.288 Chirality : 0.037 0.134 2016 Planarity : 0.005 0.041 2016 Dihedral : 4.718 34.268 1664 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.58 % Allowed : 18.07 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1500 helix: 1.09 (0.15), residues: 1188 sheet: None (None), residues: 0 loop : -2.62 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 107 TYR 0.009 0.001 TYR B 380 PHE 0.026 0.001 PHE C 371 TRP 0.021 0.002 TRP C 158 HIS 0.002 0.001 HIS C 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (12416) covalent geometry : angle 0.56639 / 0.29 (16840) hydrogen bonds : bond 0.05798 / 3.80 ( 928) hydrogen bonds : angle 3.79580 / 2.76 ( 2784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 183 PHE cc_start: 0.7894 (t80) cc_final: 0.7633 (t80) REVERT: A 355 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6762 (mp) REVERT: B 191 ASP cc_start: 0.7692 (p0) cc_final: 0.7419 (p0) REVERT: B 222 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7254 (ttt) REVERT: B 345 TYR cc_start: 0.6944 (t80) cc_final: 0.6619 (t80) REVERT: B 355 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6623 (mp) REVERT: B 371 PHE cc_start: 0.7968 (t80) cc_final: 0.7747 (t80) REVERT: C 191 ASP cc_start: 0.7431 (p0) cc_final: 0.7145 (p0) REVERT: C 355 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6518 (mp) REVERT: D 183 PHE cc_start: 0.7977 (t80) cc_final: 0.7751 (t80) REVERT: D 191 ASP cc_start: 0.7906 (p0) cc_final: 0.7619 (p0) REVERT: D 355 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6799 (mp) REVERT: D 371 PHE cc_start: 0.7791 (t80) cc_final: 0.7567 (t80) outliers start: 35 outliers final: 12 residues processed: 215 average time/residue: 0.3102 time to fit residues: 76.5773 Evaluate side-chains 178 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 82 optimal weight: 0.9990 chunk 29 optimal weight: 0.0070 chunk 26 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117388 restraints weight = 17830.222| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.40 r_work: 0.3420 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12416 Z= 0.124 Angle : 0.541 8.653 16840 Z= 0.266 Chirality : 0.037 0.134 2016 Planarity : 0.003 0.032 2016 Dihedral : 4.167 27.637 1658 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.88 % Allowed : 20.21 % Favored : 76.92 % 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: 1.43 (0.22), residues: 1500 helix: 1.69 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -2.46 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 18 TYR 0.008 0.001 TYR D 115 PHE 0.024 0.001 PHE C 50 TRP 0.019 0.002 TRP C 158 HIS 0.002 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (12416) covalent geometry : angle 0.54125 / 0.27 (16840) hydrogen bonds : bond 0.05044 / 3.31 ( 928) hydrogen bonds : angle 3.48779 / 2.53 ( 2784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.479 Fit side-chains REVERT: A 191 ASP cc_start: 0.7738 (p0) cc_final: 0.7446 (p0) REVERT: A 222 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7224 (ttt) REVERT: A 355 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6506 (mp) REVERT: A 377 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6594 (mtt) REVERT: B 191 ASP cc_start: 0.7827 (p0) cc_final: 0.7467 (p0) REVERT: B 345 TYR cc_start: 0.6743 (t80) cc_final: 0.6540 (t80) REVERT: B 355 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6405 (mp) REVERT: B 371 PHE cc_start: 0.7856 (t80) cc_final: 0.7616 (t80) REVERT: C 191 ASP cc_start: 0.7413 (p0) cc_final: 0.7150 (p0) REVERT: C 355 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6240 (mp) REVERT: C 371 PHE cc_start: 0.7713 (t80) cc_final: 0.7450 (t80) REVERT: D 183 PHE cc_start: 0.7886 (t80) cc_final: 0.7560 (t80) REVERT: D 191 ASP cc_start: 0.7883 (p0) cc_final: 0.7566 (p0) REVERT: D 355 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6539 (mp) REVERT: D 371 PHE cc_start: 0.7807 (t80) cc_final: 0.7583 (t80) outliers start: 39 outliers final: 19 residues processed: 219 average time/residue: 0.2934 time to fit residues: 74.3564 Evaluate side-chains 186 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 HIS C 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.148045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117135 restraints weight = 17835.374| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.32 r_work: 0.3367 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12416 Z= 0.144 Angle : 0.555 9.605 16840 Z= 0.272 Chirality : 0.037 0.135 2016 Planarity : 0.003 0.029 2016 Dihedral : 3.940 28.495 1658 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.54 % Allowed : 21.98 % Favored : 74.48 % 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: 1.84 (0.22), residues: 1500 helix: 1.97 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -2.27 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 18 TYR 0.009 0.001 TYR D 342 PHE 0.025 0.001 PHE C 50 TRP 0.024 0.002 TRP B 187 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12416) covalent geometry : angle 0.55491 / 0.27 (16840) hydrogen bonds : bond 0.05358 / 3.51 ( 928) hydrogen bonds : angle 3.48218 / 2.54 ( 2784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.549 Fit side-chains REVERT: A 191 ASP cc_start: 0.7967 (p0) cc_final: 0.7690 (p0) REVERT: A 355 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6620 (mp) REVERT: A 377 MET cc_start: 0.6973 (mtt) cc_final: 0.6768 (mtt) REVERT: B 183 PHE cc_start: 0.7953 (t80) cc_final: 0.7703 (t80) REVERT: B 355 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6275 (mp) REVERT: B 371 PHE cc_start: 0.8184 (t80) cc_final: 0.7983 (t80) REVERT: C 191 ASP cc_start: 0.7636 (p0) cc_final: 0.7425 (p0) REVERT: C 355 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6277 (mp) REVERT: C 371 PHE cc_start: 0.7765 (t80) cc_final: 0.7484 (t80) REVERT: D 183 PHE cc_start: 0.7989 (t80) cc_final: 0.7629 (t80) REVERT: D 191 ASP cc_start: 0.8054 (p0) cc_final: 0.7808 (p0) REVERT: D 355 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6574 (mp) REVERT: D 371 PHE cc_start: 0.7956 (t80) cc_final: 0.7735 (t80) outliers start: 48 outliers final: 28 residues processed: 205 average time/residue: 0.2721 time to fit residues: 64.9576 Evaluate side-chains 189 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 123 optimal weight: 0.2980 chunk 39 optimal weight: 0.0040 chunk 76 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS B 46 HIS B 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118335 restraints weight = 17870.660| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.34 r_work: 0.3371 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12416 Z= 0.132 Angle : 0.545 8.626 16840 Z= 0.266 Chirality : 0.037 0.134 2016 Planarity : 0.003 0.028 2016 Dihedral : 3.845 29.091 1658 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.17 % Allowed : 22.27 % Favored : 74.56 % 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: 2.11 (0.22), residues: 1500 helix: 2.13 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : -2.08 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.010 0.001 TYR A 345 PHE 0.025 0.001 PHE C 50 TRP 0.025 0.002 TRP B 187 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (12416) covalent geometry : angle 0.54524 / 0.27 (16840) hydrogen bonds : bond 0.05097 / 3.35 ( 928) hydrogen bonds : angle 3.46002 / 2.52 ( 2784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.460 Fit side-chains REVERT: A 191 ASP cc_start: 0.8155 (p0) cc_final: 0.7836 (p0) REVERT: A 377 MET cc_start: 0.6948 (mtt) cc_final: 0.6742 (mtt) REVERT: B 183 PHE cc_start: 0.7982 (t80) cc_final: 0.7737 (t80) REVERT: B 197 MET cc_start: 0.5239 (OUTLIER) cc_final: 0.5036 (tmm) REVERT: B 355 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6246 (mp) REVERT: B 371 PHE cc_start: 0.8044 (t80) cc_final: 0.7817 (t80) REVERT: B 377 MET cc_start: 0.6904 (mtt) cc_final: 0.6703 (mtt) REVERT: C 191 ASP cc_start: 0.7885 (p0) cc_final: 0.7637 (p0) REVERT: C 355 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6222 (mp) REVERT: C 371 PHE cc_start: 0.7851 (t80) cc_final: 0.7568 (t80) REVERT: D 355 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6379 (mp) REVERT: D 371 PHE cc_start: 0.8033 (t80) cc_final: 0.7829 (t80) REVERT: D 377 MET cc_start: 0.6947 (mtt) cc_final: 0.6742 (mtt) outliers start: 43 outliers final: 25 residues processed: 194 average time/residue: 0.2825 time to fit residues: 63.7239 Evaluate side-chains 194 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 99 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN B 467 GLN D 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.148403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117271 restraints weight = 17831.021| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.34 r_work: 0.3360 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12416 Z= 0.139 Angle : 0.559 10.259 16840 Z= 0.272 Chirality : 0.037 0.134 2016 Planarity : 0.003 0.026 2016 Dihedral : 3.786 28.865 1658 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.58 % Allowed : 23.01 % Favored : 74.41 % 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: 2.32 (0.22), residues: 1500 helix: 2.27 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.94 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.010 0.001 TYR A 99 PHE 0.026 0.001 PHE C 50 TRP 0.027 0.002 TRP D 187 HIS 0.003 0.001 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12416) covalent geometry : angle 0.55862 / 0.27 (16840) hydrogen bonds : bond 0.05173 / 3.40 ( 928) hydrogen bonds : angle 3.46771 / 2.53 ( 2784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.477 Fit side-chains REVERT: A 191 ASP cc_start: 0.8304 (p0) cc_final: 0.7932 (p0) REVERT: B 183 PHE cc_start: 0.8014 (t80) cc_final: 0.7775 (t80) REVERT: B 355 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6236 (mp) REVERT: B 371 PHE cc_start: 0.8045 (t80) cc_final: 0.7816 (t80) REVERT: C 190 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: C 197 MET cc_start: 0.5801 (tpt) cc_final: 0.5577 (ttm) REVERT: C 355 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6275 (mp) REVERT: C 371 PHE cc_start: 0.7933 (t80) cc_final: 0.7663 (t80) REVERT: D 355 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6385 (mp) outliers start: 35 outliers final: 23 residues processed: 193 average time/residue: 0.2648 time to fit residues: 59.3715 Evaluate side-chains 190 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 41 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 467 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.150457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119082 restraints weight = 17865.991| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.38 r_work: 0.3377 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12416 Z= 0.128 Angle : 0.568 10.464 16840 Z= 0.272 Chirality : 0.037 0.137 2016 Planarity : 0.003 0.025 2016 Dihedral : 3.747 28.864 1658 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.21 % Allowed : 24.26 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.22), residues: 1500 helix: 2.39 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.013 0.001 TYR B 188 PHE 0.027 0.001 PHE C 50 TRP 0.030 0.002 TRP D 187 HIS 0.002 0.000 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (12416) covalent geometry : angle 0.56775 / 0.27 (16840) hydrogen bonds : bond 0.04887 / 3.22 ( 928) hydrogen bonds : angle 3.39803 / 2.48 ( 2784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.286 Fit side-chains REVERT: A 191 ASP cc_start: 0.8302 (p0) cc_final: 0.7901 (p0) REVERT: B 183 PHE cc_start: 0.7971 (t80) cc_final: 0.7662 (t80) REVERT: B 355 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6180 (mp) REVERT: B 371 PHE cc_start: 0.8034 (t80) cc_final: 0.7805 (t80) REVERT: C 107 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7706 (mmm160) REVERT: C 355 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6175 (mp) REVERT: C 371 PHE cc_start: 0.7936 (t80) cc_final: 0.7670 (t80) REVERT: D 183 PHE cc_start: 0.8067 (t80) cc_final: 0.7742 (t80) REVERT: D 355 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6384 (mp) outliers start: 30 outliers final: 20 residues processed: 194 average time/residue: 0.2902 time to fit residues: 64.9193 Evaluate side-chains 193 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 467 GLN C 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116995 restraints weight = 17915.019| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.36 r_work: 0.3357 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12416 Z= 0.143 Angle : 0.598 9.398 16840 Z= 0.285 Chirality : 0.037 0.151 2016 Planarity : 0.003 0.025 2016 Dihedral : 3.599 28.155 1654 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.36 % Allowed : 25.52 % Favored : 72.12 % 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: 2.52 (0.22), residues: 1500 helix: 2.38 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.74 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 18 TYR 0.012 0.001 TYR B 188 PHE 0.027 0.001 PHE A 50 TRP 0.031 0.002 TRP B 187 HIS 0.003 0.001 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12416) covalent geometry : angle 0.59784 / 0.29 (16840) hydrogen bonds : bond 0.05153 / 3.39 ( 928) hydrogen bonds : angle 3.45591 / 2.52 ( 2784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.418 Fit side-chains REVERT: A 191 ASP cc_start: 0.8348 (p0) cc_final: 0.7951 (p0) REVERT: B 183 PHE cc_start: 0.7929 (t80) cc_final: 0.7677 (t80) REVERT: B 197 MET cc_start: 0.5705 (tmm) cc_final: 0.5390 (tmm) REVERT: B 355 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6200 (mp) REVERT: B 371 PHE cc_start: 0.8205 (t80) cc_final: 0.8003 (t80) REVERT: C 107 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7675 (mmm160) REVERT: C 355 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6232 (mp) REVERT: C 371 PHE cc_start: 0.7910 (t80) cc_final: 0.7642 (t80) REVERT: D 355 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6332 (mp) outliers start: 32 outliers final: 24 residues processed: 186 average time/residue: 0.3125 time to fit residues: 66.6545 Evaluate side-chains 189 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 103 optimal weight: 0.1980 chunk 132 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN C 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.148839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116975 restraints weight = 17874.467| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.41 r_work: 0.3349 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12416 Z= 0.144 Angle : 0.598 9.506 16840 Z= 0.287 Chirality : 0.037 0.145 2016 Planarity : 0.003 0.025 2016 Dihedral : 3.608 28.085 1654 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.92 % Allowed : 26.33 % Favored : 71.76 % 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: 2.54 (0.22), residues: 1500 helix: 2.39 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.67 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 18 TYR 0.016 0.001 TYR D 188 PHE 0.028 0.001 PHE A 50 TRP 0.034 0.002 TRP B 187 HIS 0.003 0.001 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12416) covalent geometry : angle 0.59822 / 0.29 (16840) hydrogen bonds : bond 0.05173 / 3.41 ( 928) hydrogen bonds : angle 3.46386 / 2.53 ( 2784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.340 Fit side-chains REVERT: A 191 ASP cc_start: 0.8358 (p0) cc_final: 0.7949 (p0) REVERT: B 183 PHE cc_start: 0.7976 (t80) cc_final: 0.7715 (t80) REVERT: B 355 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6160 (mp) REVERT: C 107 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7619 (mmm160) REVERT: C 355 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6172 (mp) REVERT: C 371 PHE cc_start: 0.7934 (t80) cc_final: 0.7668 (t80) REVERT: D 355 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6181 (mp) outliers start: 26 outliers final: 21 residues processed: 178 average time/residue: 0.3023 time to fit residues: 61.7859 Evaluate side-chains 182 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 125 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN C 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.149317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117442 restraints weight = 17935.349| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.38 r_work: 0.3359 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12416 Z= 0.142 Angle : 0.611 9.981 16840 Z= 0.289 Chirality : 0.037 0.151 2016 Planarity : 0.003 0.025 2016 Dihedral : 3.624 27.832 1654 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.92 % Allowed : 27.06 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.56 (0.22), residues: 1500 helix: 2.42 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -1.71 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 18 TYR 0.010 0.001 TYR D 188 PHE 0.029 0.001 PHE B 50 TRP 0.037 0.003 TRP D 187 HIS 0.003 0.001 HIS C 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (12416) covalent geometry : angle 0.61097 / 0.29 (16840) hydrogen bonds : bond 0.05123 / 3.38 ( 928) hydrogen bonds : angle 3.46691 / 2.54 ( 2784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.393 Fit side-chains REVERT: A 191 ASP cc_start: 0.8358 (p0) cc_final: 0.7944 (p0) REVERT: B 183 PHE cc_start: 0.8020 (t80) cc_final: 0.7809 (t80) REVERT: B 355 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6138 (mp) REVERT: C 107 ARG cc_start: 0.7925 (mmm160) cc_final: 0.7629 (mmm160) REVERT: C 355 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6146 (mp) REVERT: C 371 PHE cc_start: 0.8024 (t80) cc_final: 0.7770 (t80) REVERT: D 355 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6190 (mp) outliers start: 26 outliers final: 24 residues processed: 182 average time/residue: 0.3153 time to fit residues: 65.6643 Evaluate side-chains 188 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 146 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 120 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN B 467 GLN C 467 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.150440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118415 restraints weight = 17897.345| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.45 r_work: 0.3369 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12416 Z= 0.132 Angle : 0.607 10.034 16840 Z= 0.285 Chirality : 0.037 0.144 2016 Planarity : 0.003 0.025 2016 Dihedral : 3.604 27.200 1654 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.92 % Allowed : 27.29 % Favored : 70.80 % 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: 2.65 (0.22), residues: 1500 helix: 2.46 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.61 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.011 0.001 TYR D 188 PHE 0.034 0.001 PHE B 371 TRP 0.036 0.002 TRP D 187 HIS 0.002 0.000 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (12416) covalent geometry : angle 0.60670 / 0.28 (16840) hydrogen bonds : bond 0.04906 / 3.23 ( 928) hydrogen bonds : angle 3.42238 / 2.50 ( 2784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2979.95 seconds wall clock time: 51 minutes 49.08 seconds (3109.08 seconds total)