Starting phenix.real_space_refine on Fri Jul 3 19:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9con_45786/07_2026/9con_45786.cif Found real_map, /net/cci-nas-00/data/ceres_data/9con_45786/07_2026/9con_45786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9con_45786/07_2026/9con_45786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9con_45786/07_2026/9con_45786.map" model { file = "/net/cci-nas-00/data/ceres_data/9con_45786/07_2026/9con_45786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9con_45786/07_2026/9con_45786.cif" } resolution = 3.06 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= 0.001 sd= 0.040 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 60 5.16 5 C 9924 2.51 5 N 2556 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s 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: 15280 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "C" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "D" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 3.29, per 1000 atoms: 0.22 Number of scatterers: 15280 At special positions: 0 Unit cell: (117.975, 117.975, 150.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 60 16.00 O 2736 8.00 N 2556 7.00 C 9924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.04 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 566.7 milliseconds 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3520 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 53.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 154 through 166 removed outlier: 4.226A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.555A pdb=" N GLU A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 226 Processing helix chain 'A' and resid 230 through 254 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 293 through 316 removed outlier: 3.543A pdb=" N VAL A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.213A pdb=" N SER A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.812A pdb=" N GLU A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.532A pdb=" N ARG A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.981A pdb=" N LYS A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 395 through 421 Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.539A pdb=" N TRP A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.517A pdb=" N LEU A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 154 through 166 removed outlier: 4.227A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 190 through 201 removed outlier: 3.555A pdb=" N GLU C 201 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 230 through 254 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 293 through 316 removed outlier: 3.543A pdb=" N VAL C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 removed outlier: 4.213A pdb=" N SER C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.812A pdb=" N GLU C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 370 removed outlier: 3.531A pdb=" N ARG C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 379 removed outlier: 3.982A pdb=" N LYS C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 395 through 421 Processing helix chain 'C' and resid 430 through 443 removed outlier: 4.539A pdb=" N TRP C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.517A pdb=" N LEU C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 154 through 166 removed outlier: 4.227A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.555A pdb=" N GLU B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 226 Processing helix chain 'B' and resid 230 through 254 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 293 through 316 removed outlier: 3.542A pdb=" N VAL B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 removed outlier: 4.213A pdb=" N SER B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.813A pdb=" N GLU B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 370 removed outlier: 3.532A pdb=" N ARG B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.981A pdb=" N LYS B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 395 through 421 Processing helix chain 'B' and resid 430 through 443 removed outlier: 4.539A pdb=" N TRP B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.517A pdb=" N LEU B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 154 through 166 removed outlier: 4.227A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 Processing helix chain 'D' and resid 190 through 201 removed outlier: 3.555A pdb=" N GLU D 201 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 230 through 254 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.543A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 removed outlier: 4.214A pdb=" N SER D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.813A pdb=" N GLU D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 370 removed outlier: 3.532A pdb=" N ARG D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 379 removed outlier: 3.981A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 395 through 421 Processing helix chain 'D' and resid 430 through 443 removed outlier: 4.539A pdb=" N TRP D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.517A pdb=" N LEU D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 8 Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.227A pdb=" N GLY E 11 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 53 " --> pdb=" O SER E 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.227A pdb=" N GLY E 11 " --> pdb=" O THR E 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 110 Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 110 Processing sheet with id=AA7, first strand: chain 'D' and resid 105 through 110 Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 8 Processing sheet with id=AA9, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.227A pdb=" N GLY F 11 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F 53 " --> pdb=" O SER F 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER F 57 " --> pdb=" O ARG F 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.227A pdb=" N GLY F 11 " --> pdb=" O THR F 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 8 Processing sheet with id=AB3, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.227A pdb=" N GLY G 11 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG G 53 " --> pdb=" O SER G 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.227A pdb=" N GLY G 11 " --> pdb=" O THR G 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.228A pdb=" N GLY H 11 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG H 39 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG H 53 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER H 57 " --> pdb=" O ARG H 53 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.228A pdb=" N GLY H 11 " --> pdb=" O THR H 114 " (cutoff:3.500A) 864 hydrogen bonds defined for protein. 2388 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: 2.56 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3706 1.33 - 1.45: 3311 1.45 - 1.57: 8535 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 15644 Sorted by residual: bond pdb=" CA SER F 34 " pdb=" CB SER F 34 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.66e-02 3.63e+03 1.62e+01 bond pdb=" CA SER H 34 " pdb=" CB SER H 34 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.66e-02 3.63e+03 1.62e+01 bond pdb=" CA SER G 34 " pdb=" CB SER G 34 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.66e-02 3.63e+03 1.62e+01 bond pdb=" N LYS E 87 " pdb=" CA LYS E 87 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.61e+01 bond pdb=" N LYS G 87 " pdb=" CA LYS G 87 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.61e+01 ... (remaining 15639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 19276 2.01 - 4.02: 1621 4.02 - 6.03: 235 6.03 - 8.03: 44 8.03 - 10.04: 4 Bond angle restraints: 21180 Sorted by residual: angle pdb=" CA PHE D 115 " pdb=" CB PHE D 115 " pdb=" CG PHE D 115 " ideal model delta sigma weight residual 113.80 118.79 -4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" CA PHE B 115 " pdb=" CB PHE B 115 " pdb=" CG PHE B 115 " ideal model delta sigma weight residual 113.80 118.78 -4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " pdb=" CG PHE A 115 " ideal model delta sigma weight residual 113.80 118.78 -4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" CA PHE C 115 " pdb=" CB PHE C 115 " pdb=" CG PHE C 115 " ideal model delta sigma weight residual 113.80 118.75 -4.95 1.00e+00 1.00e+00 2.45e+01 angle pdb=" N LYS G 76 " pdb=" CA LYS G 76 " pdb=" CB LYS G 76 " ideal model delta sigma weight residual 111.49 103.50 7.99 1.66e+00 3.63e-01 2.32e+01 ... (remaining 21175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 7814 14.24 - 28.48: 965 28.48 - 42.72: 317 42.72 - 56.95: 88 56.95 - 71.19: 40 Dihedral angle restraints: 9224 sinusoidal: 3732 harmonic: 5492 Sorted by residual: dihedral pdb=" N ARG G 32 " pdb=" C ARG G 32 " pdb=" CA ARG G 32 " pdb=" CB ARG G 32 " ideal model delta harmonic sigma weight residual 122.80 112.64 10.16 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" N ARG H 32 " pdb=" C ARG H 32 " pdb=" CA ARG H 32 " pdb=" CB ARG H 32 " ideal model delta harmonic sigma weight residual 122.80 112.67 10.13 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" N ARG E 32 " pdb=" C ARG E 32 " pdb=" CA ARG E 32 " pdb=" CB ARG E 32 " ideal model delta harmonic sigma weight residual 122.80 112.69 10.11 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 9221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1641 0.059 - 0.118: 452 0.118 - 0.177: 171 0.177 - 0.236: 56 0.236 - 0.295: 12 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CA ARG H 32 " pdb=" N ARG H 32 " pdb=" C ARG H 32 " pdb=" CB ARG H 32 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ARG G 32 " pdb=" N ARG G 32 " pdb=" C ARG G 32 " pdb=" CB ARG G 32 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ARG E 32 " pdb=" N ARG E 32 " pdb=" C ARG E 32 " pdb=" CB ARG E 32 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 2329 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 27 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C GLY G 27 " -0.059 2.00e-02 2.50e+03 pdb=" O GLY G 27 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU G 28 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 27 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C GLY H 27 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY H 27 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU H 28 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 27 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C GLY E 27 " 0.058 2.00e-02 2.50e+03 pdb=" O GLY E 27 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU E 28 " -0.020 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.82: 4790 2.82 - 3.40: 16515 3.40 - 3.98: 30231 3.98 - 4.56: 42463 4.56 - 5.14: 62596 Nonbonded interactions: 156595 Sorted by model distance: nonbonded pdb=" O THR B 390 " pdb=" OG SER B 394 " model vdw 2.245 3.040 nonbonded pdb=" O THR A 390 " pdb=" OG SER A 394 " model vdw 2.245 3.040 nonbonded pdb=" O THR D 390 " pdb=" OG SER D 394 " model vdw 2.246 3.040 nonbonded pdb=" O THR C 390 " pdb=" OG SER C 394 " model vdw 2.246 3.040 nonbonded pdb=" O VAL B 439 " pdb=" OG1 THR B 443 " model vdw 2.286 3.040 ... (remaining 156590 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 490) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.270 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 : 0.008 0.067 15648 Z= 0.580 Angle : 1.135 10.043 21188 Z= 0.800 Chirality : 0.069 0.295 2332 Planarity : 0.011 0.126 2700 Dihedral : 14.862 71.193 5692 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.49 % Allowed : 16.02 % Favored : 81.49 % Cbeta Deviations : 0.23 % 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: -0.41 (0.20), residues: 1876 helix: 0.69 (0.19), residues: 856 sheet: -1.36 (0.40), residues: 156 loop : -1.00 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 325 TYR 0.018 0.002 TYR B 265 PHE 0.022 0.002 PHE D 115 TRP 0.011 0.003 TRP C 436 HIS 0.001 0.000 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.58 (15644) covalent geometry : angle 1.13292 / 0.80 (21180) SS BOND : bond 0.00989 / 0.61 ( 4) SS BOND : angle 3.32785 / 1.80 ( 8) hydrogen bonds : bond 0.21558 / 13.80 ( 848) hydrogen bonds : angle 7.66672 / 5.41 ( 2388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.465 Fit side-chains REVERT: A 147 TYR cc_start: 0.7384 (m-80) cc_final: 0.7026 (m-80) REVERT: E 46 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6447 (ttm-80) REVERT: C 147 TYR cc_start: 0.7370 (m-80) cc_final: 0.7100 (m-80) REVERT: B 147 TYR cc_start: 0.7370 (m-80) cc_final: 0.7039 (m-80) REVERT: D 147 TYR cc_start: 0.7370 (m-80) cc_final: 0.7050 (m-80) REVERT: F 46 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6428 (ttm-80) REVERT: G 46 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6443 (ttm-80) REVERT: H 46 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6467 (ttm-80) outliers start: 41 outliers final: 17 residues processed: 259 average time/residue: 0.1126 time to fit residues: 42.5505 Evaluate side-chains 214 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 46 ARG Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 64 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 59 ASN F 59 ASN F 82 GLN G 59 ASN G 82 GLN H 59 ASN H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.182019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.140779 restraints weight = 15490.114| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.47 r_work: 0.3099 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15648 Z= 0.142 Angle : 0.583 6.207 21188 Z= 0.312 Chirality : 0.041 0.159 2332 Planarity : 0.006 0.054 2700 Dihedral : 6.216 59.558 2163 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.37 % Allowed : 18.14 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1876 helix: 1.40 (0.18), residues: 896 sheet: -1.51 (0.29), residues: 232 loop : -0.11 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 325 TYR 0.012 0.002 TYR D 163 PHE 0.013 0.001 PHE A 435 TRP 0.011 0.001 TRP A 436 HIS 0.001 0.000 HIS D 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15644) covalent geometry : angle 0.58199 / 0.31 (21180) SS BOND : bond 0.00277 / 0.17 ( 4) SS BOND : angle 1.77935 / 0.90 ( 8) hydrogen bonds : bond 0.05006 / 3.17 ( 848) hydrogen bonds : angle 4.88894 / 3.48 ( 2388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.599 Fit side-chains REVERT: A 263 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7685 (mttt) REVERT: A 319 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8231 (p) REVERT: E 46 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7020 (ttm-80) REVERT: C 186 PHE cc_start: 0.8087 (t80) cc_final: 0.7862 (t80) REVERT: C 263 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7680 (mttt) REVERT: C 319 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 186 PHE cc_start: 0.8078 (t80) cc_final: 0.7855 (t80) REVERT: B 222 LEU cc_start: 0.7350 (mt) cc_final: 0.7127 (mm) REVERT: B 262 GLU cc_start: 0.7973 (mp0) cc_final: 0.7772 (pm20) REVERT: B 263 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7686 (mttt) REVERT: B 319 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8192 (p) REVERT: D 186 PHE cc_start: 0.8065 (t80) cc_final: 0.7860 (t80) REVERT: D 263 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7708 (mttt) REVERT: D 319 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8217 (p) REVERT: F 46 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7030 (ttm-80) REVERT: G 46 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7032 (ttm-80) REVERT: H 46 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7036 (ttm-80) outliers start: 39 outliers final: 23 residues processed: 233 average time/residue: 0.1253 time to fit residues: 43.3834 Evaluate side-chains 219 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain B residue 263 LYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 46 ARG Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 46 ARG Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 46 ARG Chi-restraints excluded: chain H residue 59 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 92 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.183015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.147067 restraints weight = 15509.984| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.38 r_work: 0.3039 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15648 Z= 0.156 Angle : 0.547 6.362 21188 Z= 0.291 Chirality : 0.042 0.148 2332 Planarity : 0.005 0.056 2700 Dihedral : 6.073 59.353 2152 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.03 % Allowed : 17.42 % Favored : 79.55 % 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: 0.82 (0.20), residues: 1876 helix: 1.54 (0.18), residues: 876 sheet: -0.92 (0.28), residues: 236 loop : -0.02 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 100 TYR 0.014 0.002 TYR D 163 PHE 0.018 0.001 PHE A 186 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15644) covalent geometry : angle 0.54538 / 0.29 (21180) SS BOND : bond 0.00378 / 0.23 ( 4) SS BOND : angle 1.96029 / 1.02 ( 8) hydrogen bonds : bond 0.04462 / 2.86 ( 848) hydrogen bonds : angle 4.55253 / 3.23 ( 2388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 0.618 Fit side-chains REVERT: A 114 ARG cc_start: 0.7703 (mmt-90) cc_final: 0.7419 (mmt90) REVERT: A 186 PHE cc_start: 0.8150 (t80) cc_final: 0.7714 (t80) REVERT: A 222 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6981 (mp) REVERT: A 263 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7637 (mttt) REVERT: A 319 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8186 (p) REVERT: C 222 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.7003 (mp) REVERT: C 253 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8648 (mp) REVERT: C 263 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7652 (mttt) REVERT: C 319 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 222 LEU cc_start: 0.7238 (mt) cc_final: 0.7027 (mm) REVERT: B 263 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7627 (mttt) REVERT: B 319 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8155 (p) REVERT: D 114 ARG cc_start: 0.7677 (mmt-90) cc_final: 0.7377 (mmt90) REVERT: D 222 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7015 (mp) REVERT: D 253 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8628 (mp) REVERT: D 263 LYS cc_start: 0.8374 (mtpp) cc_final: 0.7660 (mttt) REVERT: D 319 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8170 (p) outliers start: 50 outliers final: 24 residues processed: 233 average time/residue: 0.1277 time to fit residues: 43.9947 Evaluate side-chains 211 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 59 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 6 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 20 optimal weight: 0.0170 chunk 171 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.180295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.140696 restraints weight = 15540.841| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.45 r_work: 0.2991 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15648 Z= 0.189 Angle : 0.555 5.628 21188 Z= 0.298 Chirality : 0.043 0.147 2332 Planarity : 0.005 0.057 2700 Dihedral : 5.107 59.910 2136 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.70 % Allowed : 16.93 % Favored : 79.37 % 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: 0.90 (0.20), residues: 1876 helix: 1.47 (0.18), residues: 876 sheet: -0.26 (0.31), residues: 216 loop : -0.04 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.012 0.002 TYR D 163 PHE 0.016 0.002 PHE B 186 TRP 0.008 0.001 TRP D 436 HIS 0.001 0.001 HIS D 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (15644) covalent geometry : angle 0.55387 / 0.30 (21180) SS BOND : bond 0.00491 / 0.30 ( 4) SS BOND : angle 1.99730 / 1.04 ( 8) hydrogen bonds : bond 0.04478 / 2.85 ( 848) hydrogen bonds : angle 4.49772 / 3.19 ( 2388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 0.612 Fit side-chains REVERT: A 114 ARG cc_start: 0.7705 (mmt-90) cc_final: 0.7324 (mmt90) REVERT: A 186 PHE cc_start: 0.8068 (t80) cc_final: 0.7718 (t80) REVERT: A 222 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.7030 (mp) REVERT: C 114 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7234 (mtp85) REVERT: C 222 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7058 (mp) REVERT: B 114 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7212 (mtp85) REVERT: B 222 LEU cc_start: 0.7336 (mt) cc_final: 0.7111 (mm) REVERT: D 222 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7060 (mp) outliers start: 61 outliers final: 42 residues processed: 225 average time/residue: 0.1109 time to fit residues: 37.1126 Evaluate side-chains 226 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 185 optimal weight: 2.9990 chunk 149 optimal weight: 0.0870 chunk 132 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.184060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.142562 restraints weight = 15614.738| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.55 r_work: 0.3058 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15648 Z= 0.105 Angle : 0.491 5.441 21188 Z= 0.260 Chirality : 0.040 0.134 2332 Planarity : 0.005 0.053 2700 Dihedral : 4.723 59.975 2136 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.82 % Allowed : 18.81 % Favored : 79.37 % 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: 1.17 (0.20), residues: 1876 helix: 1.77 (0.18), residues: 872 sheet: -0.30 (0.31), residues: 212 loop : 0.07 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 32 TYR 0.014 0.001 TYR A 485 PHE 0.011 0.001 PHE B 186 TRP 0.005 0.001 TRP B 305 HIS 0.000 0.000 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (15644) covalent geometry : angle 0.48979 / 0.26 (21180) SS BOND : bond 0.00236 / 0.14 ( 4) SS BOND : angle 1.77764 / 0.91 ( 8) hydrogen bonds : bond 0.03679 / 2.39 ( 848) hydrogen bonds : angle 4.29938 / 3.04 ( 2388) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.552 Fit side-chains REVERT: A 114 ARG cc_start: 0.7773 (mmt-90) cc_final: 0.7276 (mtp85) REVERT: A 186 PHE cc_start: 0.8080 (t80) cc_final: 0.7714 (t80) REVERT: A 319 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.7999 (p) REVERT: C 114 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7327 (mtp85) REVERT: C 319 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8019 (p) REVERT: B 114 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7309 (mtp85) REVERT: B 319 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.7991 (p) REVERT: D 114 ARG cc_start: 0.7714 (mtt-85) cc_final: 0.7206 (mtp85) REVERT: D 319 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.7980 (p) outliers start: 30 outliers final: 15 residues processed: 226 average time/residue: 0.1434 time to fit residues: 46.5549 Evaluate side-chains 206 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 59 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 166 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 171 optimal weight: 0.0870 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.181947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.141819 restraints weight = 15450.416| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.52 r_work: 0.3098 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15648 Z= 0.141 Angle : 0.519 6.611 21188 Z= 0.274 Chirality : 0.041 0.134 2332 Planarity : 0.006 0.070 2700 Dihedral : 4.498 59.269 2128 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.85 % Allowed : 18.39 % Favored : 78.76 % 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: 1.17 (0.20), residues: 1876 helix: 1.73 (0.18), residues: 876 sheet: -0.17 (0.31), residues: 212 loop : 0.06 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 105 TYR 0.015 0.001 TYR D 163 PHE 0.019 0.001 PHE C 148 TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (15644) covalent geometry : angle 0.51845 / 0.27 (21180) SS BOND : bond 0.00265 / 0.16 ( 4) SS BOND : angle 1.56829 / 0.81 ( 8) hydrogen bonds : bond 0.03928 / 2.53 ( 848) hydrogen bonds : angle 4.27941 / 3.03 ( 2388) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.586 Fit side-chains REVERT: A 114 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7231 (mtp85) REVERT: A 186 PHE cc_start: 0.8074 (t80) cc_final: 0.7714 (t80) REVERT: A 319 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 114 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7228 (mtp85) REVERT: C 319 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.7943 (p) REVERT: B 114 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7218 (mtp85) REVERT: B 319 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.7989 (p) REVERT: D 114 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.7116 (mtp85) REVERT: D 319 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.7963 (p) outliers start: 47 outliers final: 34 residues processed: 227 average time/residue: 0.1360 time to fit residues: 45.3013 Evaluate side-chains 222 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 106 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 135 optimal weight: 0.0010 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.182546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.142948 restraints weight = 15414.661| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.50 r_work: 0.3075 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15648 Z= 0.122 Angle : 0.501 5.733 21188 Z= 0.264 Chirality : 0.040 0.134 2332 Planarity : 0.005 0.053 2700 Dihedral : 4.416 57.987 2128 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.85 % Allowed : 18.69 % Favored : 78.46 % 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: 1.19 (0.20), residues: 1876 helix: 1.78 (0.18), residues: 876 sheet: -0.17 (0.29), residues: 216 loop : 0.04 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 32 TYR 0.017 0.001 TYR C 147 PHE 0.030 0.001 PHE C 140 TRP 0.006 0.001 TRP C 436 HIS 0.001 0.000 HIS C 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15644) covalent geometry : angle 0.50067 / 0.26 (21180) SS BOND : bond 0.00233 / 0.14 ( 4) SS BOND : angle 1.36533 / 0.71 ( 8) hydrogen bonds : bond 0.03746 / 2.42 ( 848) hydrogen bonds : angle 4.23980 / 3.00 ( 2388) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 0.587 Fit side-chains REVERT: A 114 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7287 (mtp85) REVERT: A 204 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5554 (tp) REVERT: A 319 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.7939 (p) REVERT: E 47 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: C 114 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7316 (mtp85) REVERT: C 186 PHE cc_start: 0.8038 (t80) cc_final: 0.7715 (t80) REVERT: C 204 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5571 (tp) REVERT: C 319 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 114 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7290 (mtp85) REVERT: B 146 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6893 (mt-10) REVERT: B 186 PHE cc_start: 0.8022 (t80) cc_final: 0.7722 (t80) REVERT: B 204 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5580 (tp) REVERT: B 319 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.7999 (p) REVERT: D 114 ARG cc_start: 0.7656 (mtt-85) cc_final: 0.7164 (mtp85) REVERT: D 186 PHE cc_start: 0.8013 (t80) cc_final: 0.7694 (t80) REVERT: D 319 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.7959 (p) REVERT: F 47 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: G 47 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7875 (mt-10) outliers start: 47 outliers final: 30 residues processed: 235 average time/residue: 0.1370 time to fit residues: 47.3299 Evaluate side-chains 230 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 160 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.179995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.139610 restraints weight = 15657.439| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.51 r_work: 0.3022 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15648 Z= 0.149 Angle : 0.524 7.031 21188 Z= 0.277 Chirality : 0.041 0.137 2332 Planarity : 0.005 0.053 2700 Dihedral : 4.428 57.116 2128 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.16 % Allowed : 18.45 % Favored : 78.40 % 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: 1.16 (0.20), residues: 1876 helix: 1.71 (0.18), residues: 876 sheet: -0.09 (0.30), residues: 216 loop : 0.06 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 32 TYR 0.015 0.001 TYR D 163 PHE 0.015 0.001 PHE C 148 TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS D 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (15644) covalent geometry : angle 0.52291 / 0.28 (21180) SS BOND : bond 0.00336 / 0.20 ( 4) SS BOND : angle 1.57017 / 0.82 ( 8) hydrogen bonds : bond 0.03944 / 2.54 ( 848) hydrogen bonds : angle 4.25857 / 3.02 ( 2388) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.608 Fit side-chains REVERT: A 114 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7544 (mmt90) REVERT: A 186 PHE cc_start: 0.8129 (t80) cc_final: 0.7746 (t80) REVERT: A 204 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5541 (tp) REVERT: E 47 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: C 114 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7290 (mtp85) REVERT: C 186 PHE cc_start: 0.8007 (t80) cc_final: 0.7685 (t80) REVERT: B 114 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7250 (mtp85) REVERT: B 146 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6788 (mt-10) REVERT: B 186 PHE cc_start: 0.8025 (t80) cc_final: 0.7711 (t80) REVERT: B 319 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.7960 (p) REVERT: D 114 ARG cc_start: 0.7683 (mtt-85) cc_final: 0.7432 (mmt90) REVERT: D 186 PHE cc_start: 0.7991 (t80) cc_final: 0.7663 (t80) REVERT: D 319 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.7964 (p) REVERT: F 47 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: H 47 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7913 (mt-10) outliers start: 52 outliers final: 34 residues processed: 234 average time/residue: 0.1381 time to fit residues: 47.5022 Evaluate side-chains 232 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.181520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.141780 restraints weight = 15447.736| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.56 r_work: 0.3034 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15648 Z= 0.138 Angle : 0.514 6.219 21188 Z= 0.273 Chirality : 0.041 0.135 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.414 56.501 2128 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.16 % Allowed : 17.78 % Favored : 79.07 % 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: 1.15 (0.19), residues: 1876 helix: 1.74 (0.18), residues: 876 sheet: -0.15 (0.29), residues: 216 loop : 0.02 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 170 TYR 0.017 0.001 TYR C 147 PHE 0.024 0.001 PHE C 140 TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (15644) covalent geometry : angle 0.51375 / 0.27 (21180) SS BOND : bond 0.00284 / 0.17 ( 4) SS BOND : angle 1.46224 / 0.76 ( 8) hydrogen bonds : bond 0.03871 / 2.50 ( 848) hydrogen bonds : angle 4.25104 / 3.02 ( 2388) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.526 Fit side-chains REVERT: A 114 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7190 (mtp85) REVERT: A 186 PHE cc_start: 0.8097 (t80) cc_final: 0.7682 (t80) REVERT: A 204 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5558 (tp) REVERT: A 319 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.7915 (p) REVERT: E 47 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: E 76 LYS cc_start: 0.7692 (tttt) cc_final: 0.7478 (tttt) REVERT: C 114 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7232 (mtp85) REVERT: C 146 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7113 (mt-10) REVERT: C 186 PHE cc_start: 0.7994 (t80) cc_final: 0.7677 (t80) REVERT: B 114 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7204 (mtp85) REVERT: B 146 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6826 (mt-10) REVERT: B 186 PHE cc_start: 0.8001 (t80) cc_final: 0.7697 (t80) REVERT: D 114 ARG cc_start: 0.7579 (mtt-85) cc_final: 0.7319 (mmt90) REVERT: D 186 PHE cc_start: 0.7982 (t80) cc_final: 0.7656 (t80) REVERT: F 47 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: G 47 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: H 47 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7883 (mt-10) outliers start: 52 outliers final: 35 residues processed: 237 average time/residue: 0.1393 time to fit residues: 48.1874 Evaluate side-chains 227 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 429 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 171 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 0.0770 chunk 115 optimal weight: 0.0980 chunk 112 optimal weight: 0.0270 chunk 155 optimal weight: 0.0770 chunk 135 optimal weight: 0.0040 chunk 17 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 overall best weight: 0.0566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.188177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.149934 restraints weight = 15606.375| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.47 r_work: 0.3146 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15648 Z= 0.096 Angle : 0.487 6.715 21188 Z= 0.257 Chirality : 0.039 0.126 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.186 53.927 2128 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.94 % Allowed : 18.99 % Favored : 79.07 % 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: 1.40 (0.20), residues: 1876 helix: 1.98 (0.18), residues: 892 sheet: 0.00 (0.29), residues: 216 loop : 0.03 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 32 TYR 0.013 0.001 TYR D 163 PHE 0.014 0.001 PHE D 148 TRP 0.005 0.001 TRP G 37 HIS 0.000 0.000 HIS D 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (15644) covalent geometry : angle 0.48676 / 0.26 (21180) SS BOND : bond 0.00390 / 0.21 ( 4) SS BOND : angle 1.32121 / 0.67 ( 8) hydrogen bonds : bond 0.03263 / 2.13 ( 848) hydrogen bonds : angle 4.09565 / 2.89 ( 2388) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.605 Fit side-chains REVERT: A 319 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.7941 (p) REVERT: E 47 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: C 114 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7134 (mtp85) REVERT: C 146 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7121 (mt-10) REVERT: C 186 PHE cc_start: 0.7959 (t80) cc_final: 0.7672 (t80) REVERT: C 319 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 402 ILE cc_start: 0.8293 (mt) cc_final: 0.8088 (mm) REVERT: B 114 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7119 (mtp85) REVERT: B 146 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6901 (mt-10) REVERT: B 182 GLU cc_start: 0.7368 (tt0) cc_final: 0.6668 (tp30) REVERT: B 186 PHE cc_start: 0.7938 (t80) cc_final: 0.7722 (t80) REVERT: B 319 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.7945 (p) REVERT: D 114 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.7235 (mmt90) REVERT: D 186 PHE cc_start: 0.7935 (t80) cc_final: 0.7654 (t80) REVERT: D 319 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.7952 (p) REVERT: F 47 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: G 47 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: H 47 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7764 (mt-10) outliers start: 32 outliers final: 16 residues processed: 249 average time/residue: 0.1388 time to fit residues: 50.4559 Evaluate side-chains 232 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 44 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 183 optimal weight: 0.0980 chunk 17 optimal weight: 0.0980 chunk 109 optimal weight: 0.0570 chunk 137 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.185490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144913 restraints weight = 15384.251| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.47 r_work: 0.3079 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15648 Z= 0.110 Angle : 0.498 6.268 21188 Z= 0.262 Chirality : 0.040 0.131 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.100 50.832 2128 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.76 % Allowed : 19.36 % Favored : 78.88 % 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: 1.48 (0.20), residues: 1876 helix: 2.01 (0.18), residues: 892 sheet: 0.15 (0.30), residues: 216 loop : 0.08 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 32 TYR 0.014 0.001 TYR B 147 PHE 0.020 0.001 PHE B 148 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS B 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15644) covalent geometry : angle 0.49648 / 0.26 (21180) SS BOND : bond 0.00372 / 0.20 ( 4) SS BOND : angle 1.81991 / 0.93 ( 8) hydrogen bonds : bond 0.03481 / 2.25 ( 848) hydrogen bonds : angle 4.08027 / 2.89 ( 2388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4717.76 seconds wall clock time: 81 minutes 22.28 seconds (4882.28 seconds total)