Starting phenix.real_space_refine on Wed Mar 4 08:16:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lid_23374/03_2026/7lid_23374.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lid_23374/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lid_23374/03_2026/7lid_23374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lid_23374/03_2026/7lid_23374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lid_23374/03_2026/7lid_23374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lid_23374/03_2026/7lid_23374.map" } 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-5986/lib/python3.9/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: 2.53, per 1000 atoms: 0.21 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: 0.90 Conformation dependent library (CDL) restraints added in 695.1 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: 0.28 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: 1.79 Time building geometry restraints manager: 1.25 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: 28 71.96 - 89.96: 4 Dihedral angle restraints: 7284 sinusoidal: 2776 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 7281 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: 0.03 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: 2.570 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.090 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 : 15.329 89.956 4356 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 covalent geometry : bond 0.00643 (12416) covalent geometry : angle 0.87722 (16840) hydrogen bonds : bond 0.13201 ( 928) hydrogen bonds : angle 5.04240 ( 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 : 0.473 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: 0.3895 time to fit residues: 118.0485 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 : 0.470 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3895 r_free = 0.3895 target = 0.146758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114831 restraints weight = 17782.208| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.46 r_work: 0.3384 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1613 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 : 0.570 6.536 16840 Z= 0.289 Chirality : 0.037 0.141 2016 Planarity : 0.005 0.045 2016 Dihedral : 5.999 55.375 1672 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.58 % Allowed : 18.14 % Favored : 79.28 % 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 0.025 0.001 PHE C 371 TRP 0.020 0.002 TRP C 158 HIS 0.003 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00285 (12416) covalent geometry : angle 0.56966 (16840) hydrogen bonds : bond 0.05756 ( 928) hydrogen bonds : angle 3.78674 ( 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 230 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 183 PHE cc_start: 0.7903 (t80) cc_final: 0.7638 (t80) REVERT: A 355 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6832 (mp) REVERT: A 371 PHE cc_start: 0.7843 (t80) cc_final: 0.7643 (t80) REVERT: B 191 ASP cc_start: 0.7692 (p0) cc_final: 0.7452 (p0) REVERT: B 222 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7293 (ttt) REVERT: B 345 TYR cc_start: 0.6978 (t80) cc_final: 0.6588 (t80) REVERT: B 355 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6714 (mp) REVERT: B 371 PHE cc_start: 0.7977 (t80) cc_final: 0.7752 (t80) REVERT: C 191 ASP cc_start: 0.7431 (p0) cc_final: 0.7143 (p0) REVERT: C 355 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6485 (mp) REVERT: D 183 PHE cc_start: 0.7978 (t80) cc_final: 0.7746 (t80) REVERT: D 191 ASP cc_start: 0.7885 (p0) cc_final: 0.7590 (p0) REVERT: D 355 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6835 (mp) REVERT: D 371 PHE cc_start: 0.7802 (t80) cc_final: 0.7573 (t80) outliers start: 35 outliers final: 12 residues processed: 221 average time/residue: 0.3523 time to fit residues: 88.8981 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 : 0.376 ------------------------------------------------------------------------------- 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: 0.7980 chunk 82 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN B 467 GLN C 52 GLN 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 = 0.148233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116003 restraints weight = 17863.758| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.46 r_work: 0.3371 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12416 Z= 0.129 Angle : 0.548 9.055 16840 Z= 0.270 Chirality : 0.037 0.135 2016 Planarity : 0.004 0.033 2016 Dihedral : 5.749 59.664 1666 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.17 % Allowed : 20.43 % Favored : 76.40 % 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: 1.45 (0.22), residues: 1500 helix: 1.70 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -2.42 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 18 TYR 0.008 0.001 TYR D 115 PHE 0.025 0.001 PHE C 50 TRP 0.020 0.002 TRP C 158 HIS 0.002 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00268 (12416) covalent geometry : angle 0.54822 (16840) hydrogen bonds : bond 0.05171 ( 928) hydrogen bonds : angle 3.50293 ( 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 230 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.510 Fit side-chains REVERT: A 191 ASP cc_start: 0.7737 (p0) cc_final: 0.7424 (p0) REVERT: A 355 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6583 (mp) REVERT: A 377 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6602 (mtt) REVERT: B 183 PHE cc_start: 0.7843 (t80) cc_final: 0.7580 (t80) REVERT: B 191 ASP cc_start: 0.7818 (p0) cc_final: 0.7440 (p0) REVERT: B 355 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6444 (mp) REVERT: B 371 PHE cc_start: 0.7818 (t80) cc_final: 0.7575 (t80) REVERT: C 191 ASP cc_start: 0.7454 (p0) cc_final: 0.7195 (p0) REVERT: C 355 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6248 (mp) REVERT: C 371 PHE cc_start: 0.7695 (t80) cc_final: 0.7439 (t80) REVERT: D 183 PHE cc_start: 0.7918 (t80) cc_final: 0.7608 (t80) REVERT: D 191 ASP cc_start: 0.7972 (p0) cc_final: 0.7650 (p0) REVERT: D 355 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6614 (mp) REVERT: D 371 PHE cc_start: 0.7771 (t80) cc_final: 0.7549 (t80) outliers start: 43 outliers final: 23 residues processed: 213 average time/residue: 0.3349 time to fit residues: 82.0897 Evaluate side-chains 184 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 360 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 203 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 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 C residue 468 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 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: 2.9990 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 0.0470 chunk 115 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS B 467 GLN C 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.150078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118934 restraints weight = 17730.846| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.32 r_work: 0.3389 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2553 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= 0.130 Angle : 0.545 9.000 16840 Z= 0.266 Chirality : 0.037 0.134 2016 Planarity : 0.003 0.030 2016 Dihedral : 4.801 44.197 1666 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.58 % Allowed : 22.71 % Favored : 74.71 % 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: 1.97 (0.22), residues: 1500 helix: 2.04 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : -2.20 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 18 TYR 0.009 0.001 TYR A 115 PHE 0.024 0.001 PHE C 50 TRP 0.023 0.002 TRP D 187 HIS 0.002 0.001 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00272 (12416) covalent geometry : angle 0.54547 (16840) hydrogen bonds : bond 0.05082 ( 928) hydrogen bonds : angle 3.42815 ( 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 210 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.479 Fit side-chains REVERT: A 191 ASP cc_start: 0.7983 (p0) cc_final: 0.7691 (p0) REVERT: A 355 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6482 (mp) REVERT: A 377 MET cc_start: 0.6935 (mtt) cc_final: 0.6731 (mtt) REVERT: B 183 PHE cc_start: 0.7885 (t80) cc_final: 0.7635 (t80) REVERT: B 355 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6332 (mp) REVERT: B 371 PHE cc_start: 0.8210 (t80) cc_final: 0.8008 (t80) REVERT: C 197 MET cc_start: 0.5682 (tpp) cc_final: 0.5454 (tpp) REVERT: C 355 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6229 (mp) REVERT: C 371 PHE cc_start: 0.7784 (t80) cc_final: 0.7512 (t80) REVERT: D 183 PHE cc_start: 0.8031 (t80) cc_final: 0.7687 (t80) REVERT: D 191 ASP cc_start: 0.7906 (p0) cc_final: 0.7673 (p0) REVERT: D 355 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6389 (mp) REVERT: D 371 PHE cc_start: 0.7866 (t80) cc_final: 0.7642 (t80) outliers start: 35 outliers final: 20 residues processed: 200 average time/residue: 0.2991 time to fit residues: 69.5453 Evaluate side-chains 188 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 360 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 465 LEU Chi-restraints excluded: chain C residue 104 ILE 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 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 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: 0.0670 chunk 50 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS C 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118225 restraints weight = 17868.279| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.36 r_work: 0.3378 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12416 Z= 0.133 Angle : 0.548 10.806 16840 Z= 0.266 Chirality : 0.037 0.134 2016 Planarity : 0.003 0.028 2016 Dihedral : 4.098 28.658 1666 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.02 % Allowed : 22.49 % 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: 2.22 (0.22), residues: 1500 helix: 2.21 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -2.03 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.011 0.001 TYR A 99 PHE 0.025 0.001 PHE C 50 TRP 0.025 0.002 TRP D 187 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd covalent geometry : bond 0.00287 (12416) covalent geometry : angle 0.54846 (16840) hydrogen bonds : bond 0.05100 ( 928) hydrogen bonds : angle 3.44709 ( 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 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.419 Fit side-chains REVERT: A 191 ASP cc_start: 0.8050 (p0) cc_final: 0.7710 (p0) REVERT: A 355 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6428 (mp) REVERT: A 377 MET cc_start: 0.6959 (mtt) cc_final: 0.6741 (mtt) REVERT: B 183 PHE cc_start: 0.7881 (t80) cc_final: 0.7647 (t80) REVERT: B 191 ASP cc_start: 0.7638 (p0) cc_final: 0.7420 (p0) REVERT: B 355 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6236 (mp) REVERT: B 371 PHE cc_start: 0.8038 (t80) cc_final: 0.7812 (t80) REVERT: C 355 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6233 (mp) REVERT: C 371 PHE cc_start: 0.7874 (t80) cc_final: 0.7602 (t80) REVERT: D 355 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6243 (mp) REVERT: D 371 PHE cc_start: 0.8030 (t80) cc_final: 0.7824 (t80) outliers start: 41 outliers final: 23 residues processed: 191 average time/residue: 0.3096 time to fit residues: 68.4441 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 : 0.405 ------------------------------------------------------------------------------- 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 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 190 PHE 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 143 VAL Chi-restraints excluded: chain C residue 161 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: 0.5980 chunk 119 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.149612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118346 restraints weight = 17859.052| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.36 r_work: 0.3365 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2884 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= 0.135 Angle : 0.560 9.609 16840 Z= 0.270 Chirality : 0.037 0.134 2016 Planarity : 0.003 0.026 2016 Dihedral : 4.078 28.636 1666 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.14 % Allowed : 23.16 % Favored : 74.71 % 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: 2.38 (0.22), residues: 1500 helix: 2.31 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.91 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.011 0.001 TYR A 345 PHE 0.026 0.001 PHE C 50 TRP 0.028 0.002 TRP D 187 HIS 0.003 0.001 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00292 (12416) covalent geometry : angle 0.56008 (16840) hydrogen bonds : bond 0.05098 ( 928) hydrogen bonds : angle 3.45054 ( 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 196 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.538 Fit side-chains REVERT: A 191 ASP cc_start: 0.8170 (p0) cc_final: 0.7800 (p0) REVERT: A 355 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6508 (mp) REVERT: B 183 PHE cc_start: 0.7915 (t80) cc_final: 0.7652 (t80) REVERT: B 355 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6228 (mp) REVERT: C 190 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: C 355 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6230 (mp) REVERT: C 371 PHE cc_start: 0.7877 (t80) cc_final: 0.7619 (t80) REVERT: D 355 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6234 (mp) outliers start: 29 outliers final: 20 residues processed: 184 average time/residue: 0.3200 time to fit residues: 67.9330 Evaluate side-chains 181 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 355 LEU 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 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 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 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: 3.9990 chunk 90 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.148592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117290 restraints weight = 17953.078| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.36 r_work: 0.3355 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12416 Z= 0.143 Angle : 0.582 8.952 16840 Z= 0.278 Chirality : 0.037 0.135 2016 Planarity : 0.003 0.025 2016 Dihedral : 4.095 29.361 1666 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.65 % Allowed : 23.67 % Favored : 73.67 % 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: 2.43 (0.22), residues: 1500 helix: 2.33 (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 0.002 0.000 ARG D 18 TYR 0.014 0.001 TYR B 188 PHE 0.027 0.001 PHE C 50 TRP 0.030 0.002 TRP D 187 HIS 0.003 0.001 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00317 (12416) covalent geometry : angle 0.58152 (16840) hydrogen bonds : bond 0.05225 ( 928) hydrogen bonds : angle 3.48438 ( 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 200 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.360 Fit side-chains REVERT: A 191 ASP cc_start: 0.8314 (p0) cc_final: 0.7914 (p0) REVERT: A 355 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6523 (mp) REVERT: B 183 PHE cc_start: 0.7911 (t80) cc_final: 0.7655 (t80) REVERT: B 355 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6184 (mp) REVERT: C 355 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6211 (mp) REVERT: C 371 PHE cc_start: 0.7928 (t80) cc_final: 0.7667 (t80) REVERT: C 458 MET cc_start: 0.5864 (mtm) cc_final: 0.5657 (mtp) REVERT: D 355 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6253 (mp) outliers start: 36 outliers final: 27 residues processed: 185 average time/residue: 0.3255 time to fit residues: 69.3570 Evaluate side-chains 194 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE 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 374 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 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 363 PHE Chi-restraints excluded: chain B residue 465 LEU 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 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 Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 0.0050 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 82 optimal weight: 0.0570 chunk 120 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 overall best weight: 0.2510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS C 467 GLN D 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.153299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121844 restraints weight = 17596.694| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.36 r_work: 0.3419 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12416 Z= 0.119 Angle : 0.575 9.013 16840 Z= 0.272 Chirality : 0.036 0.150 2016 Planarity : 0.003 0.025 2016 Dihedral : 4.015 26.843 1666 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.47 % Allowed : 25.74 % Favored : 72.79 % 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: 2.68 (0.23), residues: 1500 helix: 2.51 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.010 0.001 TYR B 188 PHE 0.028 0.001 PHE C 50 TRP 0.032 0.002 TRP A 187 HIS 0.001 0.000 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00234 (12416) covalent geometry : angle 0.57530 (16840) hydrogen bonds : bond 0.04549 ( 928) hydrogen bonds : angle 3.38499 ( 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 208 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.458 Fit side-chains REVERT: A 191 ASP cc_start: 0.8203 (p0) cc_final: 0.7811 (p0) REVERT: A 355 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6261 (mp) REVERT: B 183 PHE cc_start: 0.7882 (t80) cc_final: 0.7603 (t80) REVERT: B 355 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5961 (mp) REVERT: C 197 MET cc_start: 0.5454 (OUTLIER) cc_final: 0.5021 (tmm) REVERT: C 371 PHE cc_start: 0.7944 (t80) cc_final: 0.7701 (t80) REVERT: D 222 MET cc_start: 0.7219 (ttp) cc_final: 0.6996 (ttt) REVERT: D 355 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6173 (mp) outliers start: 20 outliers final: 12 residues processed: 196 average time/residue: 0.3348 time to fit residues: 75.9713 Evaluate side-chains 187 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 355 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 355 LEU 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 197 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 465 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 467 GLN D 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.150162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118773 restraints weight = 17785.549| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.37 r_work: 0.3377 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3258 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= 0.140 Angle : 0.600 9.569 16840 Z= 0.284 Chirality : 0.037 0.139 2016 Planarity : 0.003 0.026 2016 Dihedral : 3.931 27.788 1664 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.77 % Allowed : 26.92 % Favored : 71.31 % 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: 2.47 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -1.66 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 18 TYR 0.017 0.001 TYR B 461 PHE 0.027 0.001 PHE A 50 TRP 0.033 0.002 TRP B 187 HIS 0.003 0.001 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00313 (12416) covalent geometry : angle 0.60048 (16840) hydrogen bonds : bond 0.04987 ( 928) hydrogen bonds : angle 3.44245 ( 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 186 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.460 Fit side-chains REVERT: A 191 ASP cc_start: 0.8233 (p0) cc_final: 0.7820 (p0) REVERT: A 355 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6520 (mp) REVERT: B 183 PHE cc_start: 0.7921 (t80) cc_final: 0.7657 (t80) REVERT: B 355 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6168 (mp) REVERT: C 107 ARG cc_start: 0.7963 (mmm160) cc_final: 0.7659 (mmm160) REVERT: C 197 MET cc_start: 0.5513 (OUTLIER) cc_final: 0.5061 (tmm) REVERT: C 371 PHE cc_start: 0.7976 (t80) cc_final: 0.7731 (t80) REVERT: D 222 MET cc_start: 0.7289 (ttp) cc_final: 0.7055 (ttt) REVERT: D 355 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6242 (mp) REVERT: D 454 MET cc_start: 0.5832 (ttp) cc_final: 0.5609 (ttt) outliers start: 24 outliers final: 15 residues processed: 176 average time/residue: 0.3599 time to fit residues: 72.3177 Evaluate side-chains 179 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE 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 367 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 363 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 0.0060 chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 125 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 467 GLN D 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.152628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.120913 restraints weight = 17731.068| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.38 r_work: 0.3411 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3430 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= 0.125 Angle : 0.601 9.966 16840 Z= 0.281 Chirality : 0.037 0.152 2016 Planarity : 0.003 0.026 2016 Dihedral : 3.903 26.365 1664 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.40 % Allowed : 27.43 % Favored : 71.17 % 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: 2.76 (0.22), residues: 1500 helix: 2.52 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 18 TYR 0.010 0.001 TYR B 461 PHE 0.028 0.001 PHE C 50 TRP 0.038 0.002 TRP D 187 HIS 0.002 0.000 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00260 (12416) covalent geometry : angle 0.60122 (16840) hydrogen bonds : bond 0.04642 ( 928) hydrogen bonds : angle 3.39056 ( 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 199 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.469 Fit side-chains REVERT: A 191 ASP cc_start: 0.8226 (p0) cc_final: 0.7812 (p0) REVERT: A 355 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6259 (mp) REVERT: B 92 PHE cc_start: 0.6598 (m-10) cc_final: 0.6224 (m-10) REVERT: B 183 PHE cc_start: 0.7960 (t80) cc_final: 0.7683 (t80) REVERT: B 355 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6028 (mp) REVERT: C 107 ARG cc_start: 0.7925 (mmm160) cc_final: 0.7608 (mmm160) REVERT: C 197 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5030 (tmm) REVERT: C 371 PHE cc_start: 0.8006 (t80) cc_final: 0.7762 (t80) REVERT: D 222 MET cc_start: 0.7259 (ttp) cc_final: 0.7013 (ttt) REVERT: D 355 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6136 (mp) outliers start: 19 outliers final: 14 residues processed: 189 average time/residue: 0.3569 time to fit residues: 76.5596 Evaluate side-chains 189 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 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 355 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 363 PHE Chi-restraints excluded: chain C residue 419 ASP 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: 0.8980 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 0.0970 chunk 140 optimal weight: 0.8980 chunk 146 optimal weight: 0.0040 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 120 optimal weight: 0.0870 overall best weight: 0.2968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN B 233 HIS C 467 GLN D 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122614 restraints weight = 17726.573| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.41 r_work: 0.3436 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12416 Z= 0.120 Angle : 0.597 9.997 16840 Z= 0.279 Chirality : 0.037 0.196 2016 Planarity : 0.003 0.026 2016 Dihedral : 3.854 25.587 1664 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.33 % Allowed : 28.10 % Favored : 70.58 % 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: 2.82 (0.22), residues: 1500 helix: 2.54 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -1.51 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.009 0.001 TYR D 188 PHE 0.028 0.001 PHE C 50 TRP 0.036 0.002 TRP D 187 HIS 0.002 0.000 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00245 (12416) covalent geometry : angle 0.59662 (16840) hydrogen bonds : bond 0.04432 ( 928) hydrogen bonds : angle 3.35443 ( 2784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3355.17 seconds wall clock time: 58 minutes 10.72 seconds (3490.72 seconds total)