Starting phenix.real_space_refine on Thu Feb 5 06:27:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9con_45786/02_2026/9con_45786.cif Found real_map, /net/cci-nas-00/data/ceres_data/9con_45786/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9con_45786/02_2026/9con_45786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9con_45786/02_2026/9con_45786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9con_45786/02_2026/9con_45786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9con_45786/02_2026/9con_45786.map" } 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-2.0-5952/lib/python3.9/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, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.54, per 1000 atoms: 0.23 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: 1.42 Conformation dependent library (CDL) restraints added in 525.4 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: 0.43 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: 2.65 Time building geometry restraints manager: 1.87 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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.440 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 covalent geometry : bond 0.00811 (15644) covalent geometry : angle 1.13292 (21180) SS BOND : bond 0.00989 ( 4) SS BOND : angle 3.32785 ( 8) hydrogen bonds : bond 0.21558 ( 848) hydrogen bonds : angle 7.66672 ( 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 : 0.559 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: 0.1237 time to fit residues: 46.1163 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 : 0.440 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3973 r_free = 0.3973 target = 0.184746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.146936 restraints weight = 15333.164| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.41 r_work: 0.3062 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15648 Z= 0.140 Angle : 0.578 6.204 21188 Z= 0.309 Chirality : 0.041 0.153 2332 Planarity : 0.006 0.055 2700 Dihedral : 6.187 59.296 2163 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.31 % Allowed : 17.90 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1876 helix: 1.42 (0.18), residues: 876 sheet: -1.48 (0.29), residues: 232 loop : -0.23 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 325 TYR 0.012 0.002 TYR D 163 PHE 0.014 0.001 PHE A 435 TRP 0.010 0.001 TRP A 436 HIS 0.001 0.000 HIS D 488 Details of bonding type rmsd covalent geometry : bond 0.00305 (15644) covalent geometry : angle 0.57743 (21180) SS BOND : bond 0.00336 ( 4) SS BOND : angle 1.75389 ( 8) hydrogen bonds : bond 0.04828 ( 848) hydrogen bonds : angle 4.86905 ( 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 241 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.623 Fit side-chains REVERT: A 222 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.7000 (mp) REVERT: A 319 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.8149 (p) REVERT: E 46 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7008 (ttm-80) REVERT: C 186 PHE cc_start: 0.8033 (t80) cc_final: 0.7809 (t80) REVERT: C 222 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6976 (mp) REVERT: C 319 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8189 (p) REVERT: B 186 PHE cc_start: 0.8012 (t80) cc_final: 0.7784 (t80) REVERT: B 222 LEU cc_start: 0.7237 (mt) cc_final: 0.7034 (mm) REVERT: B 319 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8086 (p) REVERT: D 222 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6996 (mp) REVERT: D 319 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8119 (p) REVERT: F 46 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7001 (ttm-80) REVERT: G 46 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6971 (ttm-80) REVERT: H 46 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6974 (ttm-80) outliers start: 38 outliers final: 23 residues processed: 235 average time/residue: 0.1175 time to fit residues: 40.9579 Evaluate side-chains 217 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 222 LEU 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 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 222 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 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: 1.9990 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.183831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.144380 restraints weight = 15428.933| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.47 r_work: 0.3060 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15648 Z= 0.139 Angle : 0.532 6.121 21188 Z= 0.283 Chirality : 0.041 0.142 2332 Planarity : 0.005 0.056 2700 Dihedral : 6.044 59.689 2152 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.85 % Allowed : 18.20 % Favored : 78.94 % 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: 0.78 (0.20), residues: 1876 helix: 1.60 (0.18), residues: 876 sheet: -1.10 (0.28), residues: 236 loop : -0.11 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 32 TYR 0.013 0.001 TYR D 163 PHE 0.017 0.001 PHE A 186 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.000 HIS D 488 Details of bonding type rmsd covalent geometry : bond 0.00318 (15644) covalent geometry : angle 0.53140 (21180) SS BOND : bond 0.00285 ( 4) SS BOND : angle 1.72389 ( 8) hydrogen bonds : bond 0.04404 ( 848) hydrogen bonds : angle 4.55832 ( 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 233 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.498 Fit side-chains REVERT: A 186 PHE cc_start: 0.8096 (t80) cc_final: 0.7701 (t80) REVERT: A 222 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7019 (mp) REVERT: A 263 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7664 (mttt) REVERT: A 319 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 222 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7034 (mp) REVERT: C 263 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8134 (mmmt) REVERT: C 319 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8298 (p) REVERT: B 222 LEU cc_start: 0.7283 (mt) cc_final: 0.7057 (mm) REVERT: B 263 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7668 (mttt) REVERT: B 319 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8205 (p) REVERT: D 222 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7040 (mp) REVERT: D 263 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7670 (mttt) REVERT: D 319 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8225 (p) outliers start: 47 outliers final: 28 residues processed: 223 average time/residue: 0.1187 time to fit residues: 39.3810 Evaluate side-chains 216 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 263 LYS 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 23 CYS Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 263 LYS 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 263 LYS 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 263 LYS 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 23 CYS 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 59 ASN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 23 CYS 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: 7.9990 chunk 102 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.183588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.143812 restraints weight = 15385.610| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.53 r_work: 0.3043 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1852 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= 0.140 Angle : 0.519 5.615 21188 Z= 0.277 Chirality : 0.041 0.142 2332 Planarity : 0.005 0.055 2700 Dihedral : 4.970 59.815 2136 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.09 % Allowed : 17.48 % Favored : 79.43 % 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: 0.99 (0.20), residues: 1876 helix: 1.65 (0.18), residues: 876 sheet: -0.35 (0.31), residues: 212 loop : -0.10 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 114 TYR 0.014 0.001 TYR C 163 PHE 0.011 0.001 PHE A 186 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00326 (15644) covalent geometry : angle 0.51803 (21180) SS BOND : bond 0.00270 ( 4) SS BOND : angle 1.65754 ( 8) hydrogen bonds : bond 0.04113 ( 848) hydrogen bonds : angle 4.40409 ( 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 237 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 0.594 Fit side-chains REVERT: A 114 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7413 (mmt90) REVERT: A 186 PHE cc_start: 0.8067 (t80) cc_final: 0.7751 (t80) REVERT: A 263 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7675 (mttt) REVERT: C 114 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7253 (mtp180) REVERT: C 253 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8674 (mp) REVERT: C 263 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8122 (mmmt) REVERT: B 114 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7201 (mtp180) REVERT: B 222 LEU cc_start: 0.7338 (mt) cc_final: 0.7112 (mm) REVERT: B 263 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7665 (mttt) REVERT: D 253 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8649 (mp) REVERT: D 263 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7684 (mttt) outliers start: 51 outliers final: 25 residues processed: 222 average time/residue: 0.1245 time to fit residues: 41.4560 Evaluate side-chains 212 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 263 LYS 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 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 253 LEU Chi-restraints excluded: chain C residue 263 LYS 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 B residue 114 ARG Chi-restraints excluded: chain B residue 263 LYS 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 D residue 253 LEU Chi-restraints excluded: chain D residue 263 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 185 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 163 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.183825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.143303 restraints weight = 15471.568| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.58 r_work: 0.3053 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2074 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= 0.107 Angle : 0.487 5.358 21188 Z= 0.258 Chirality : 0.040 0.130 2332 Planarity : 0.005 0.053 2700 Dihedral : 4.701 59.962 2136 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.52 % Allowed : 19.42 % 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: 1.10 (0.20), residues: 1876 helix: 1.79 (0.18), residues: 872 sheet: -0.35 (0.30), residues: 212 loop : -0.07 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.015 0.001 TYR C 147 PHE 0.010 0.001 PHE C 148 TRP 0.005 0.001 TRP C 436 HIS 0.000 0.000 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00235 (15644) covalent geometry : angle 0.48665 (21180) SS BOND : bond 0.00014 ( 4) SS BOND : angle 1.22620 ( 8) hydrogen bonds : bond 0.03691 ( 848) hydrogen bonds : angle 4.28620 ( 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 240 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.579 Fit side-chains REVERT: A 114 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7243 (mtp85) REVERT: A 186 PHE cc_start: 0.8129 (t80) cc_final: 0.7794 (t80) REVERT: A 319 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.7950 (p) REVERT: C 114 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7282 (mtp85) REVERT: C 319 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.7974 (p) REVERT: B 114 ARG cc_start: 0.7740 (mmt-90) cc_final: 0.7225 (mtp85) REVERT: B 263 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7596 (mttt) REVERT: B 319 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.7979 (p) REVERT: D 114 ARG cc_start: 0.7709 (mmt-90) cc_final: 0.7189 (mtp85) REVERT: D 319 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.7948 (p) outliers start: 25 outliers final: 18 residues processed: 237 average time/residue: 0.1321 time to fit residues: 45.2780 Evaluate side-chains 219 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 319 SER 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 E residue 79 VAL 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 319 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain D residue 319 SER 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 F residue 79 VAL Chi-restraints excluded: chain G residue 13 VAL 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 59 ASN Chi-restraints excluded: chain H residue 79 VAL 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: 0.9990 chunk 84 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.183276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145466 restraints weight = 15343.115| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.49 r_work: 0.3004 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15648 Z= 0.146 Angle : 0.519 6.239 21188 Z= 0.275 Chirality : 0.041 0.140 2332 Planarity : 0.006 0.070 2700 Dihedral : 4.596 59.817 2132 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.76 % Allowed : 17.54 % Favored : 78.70 % 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: 1.04 (0.20), residues: 1876 helix: 1.69 (0.18), residues: 876 sheet: -0.26 (0.31), residues: 212 loop : -0.10 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 105 TYR 0.023 0.002 TYR C 147 PHE 0.019 0.001 PHE D 148 TRP 0.007 0.001 TRP C 436 HIS 0.001 0.000 HIS D 488 Details of bonding type rmsd covalent geometry : bond 0.00346 (15644) covalent geometry : angle 0.51739 (21180) SS BOND : bond 0.00368 ( 4) SS BOND : angle 1.94552 ( 8) hydrogen bonds : bond 0.03958 ( 848) hydrogen bonds : angle 4.27894 ( 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 256 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 0.581 Fit side-chains REVERT: A 114 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7161 (mtp85) REVERT: A 186 PHE cc_start: 0.8061 (t80) cc_final: 0.7816 (t80) REVERT: A 319 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.7902 (p) REVERT: A 472 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8551 (mp) REVERT: C 114 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7224 (mtp85) REVERT: C 319 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.7938 (p) REVERT: C 472 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 114 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7161 (mtp85) REVERT: B 146 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7070 (mt-10) REVERT: B 319 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.7980 (p) REVERT: B 472 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8533 (mp) REVERT: D 114 ARG cc_start: 0.7720 (mmt-90) cc_final: 0.7238 (mtp85) REVERT: D 186 PHE cc_start: 0.7921 (t80) cc_final: 0.7601 (t80) REVERT: D 319 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.7966 (p) REVERT: D 472 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8553 (mp) outliers start: 62 outliers final: 36 residues processed: 246 average time/residue: 0.1101 time to fit residues: 39.8352 Evaluate side-chains 236 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG 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 A residue 439 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 VAL 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 C residue 439 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 147 TYR 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 B residue 439 VAL Chi-restraints excluded: chain B residue 472 ILE 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 429 SER Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain F residue 13 VAL 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 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 59 ASN Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 63 optimal weight: 0.0170 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 0.0050 overall best weight: 0.8038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.181383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.140360 restraints weight = 15277.884| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.59 r_work: 0.3056 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2244 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= 0.150 Angle : 0.520 5.473 21188 Z= 0.277 Chirality : 0.041 0.142 2332 Planarity : 0.005 0.053 2700 Dihedral : 4.482 59.471 2128 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.64 % Allowed : 17.29 % 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: 1.00 (0.19), residues: 1876 helix: 1.65 (0.18), residues: 876 sheet: -0.25 (0.30), residues: 216 loop : -0.11 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 32 TYR 0.018 0.001 TYR B 147 PHE 0.020 0.001 PHE C 140 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00354 (15644) covalent geometry : angle 0.51896 (21180) SS BOND : bond 0.00364 ( 4) SS BOND : angle 1.89772 ( 8) hydrogen bonds : bond 0.04037 ( 848) hydrogen bonds : angle 4.30291 ( 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 250 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 0.540 Fit side-chains REVERT: A 114 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7525 (mmt90) REVERT: A 186 PHE cc_start: 0.8106 (t80) cc_final: 0.7815 (t80) REVERT: A 319 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.7940 (p) REVERT: A 472 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8548 (mp) REVERT: C 114 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7519 (mmt90) REVERT: C 319 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.7969 (p) REVERT: C 472 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 114 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7242 (mtp85) REVERT: B 319 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8028 (p) REVERT: B 472 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8549 (mp) REVERT: D 114 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7597 (mmt90) REVERT: D 186 PHE cc_start: 0.7988 (t80) cc_final: 0.7677 (t80) REVERT: D 319 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8003 (p) REVERT: D 472 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8550 (mp) outliers start: 60 outliers final: 35 residues processed: 237 average time/residue: 0.1161 time to fit residues: 40.5436 Evaluate side-chains 232 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG 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 A residue 439 VAL Chi-restraints excluded: chain A residue 472 ILE 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 71 SER Chi-restraints excluded: chain E residue 79 VAL 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 C residue 439 VAL Chi-restraints excluded: chain C residue 472 ILE 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 B residue 439 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain D residue 114 ARG 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 D residue 439 VAL Chi-restraints excluded: chain D residue 472 ILE 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 71 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 13 VAL 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 Chi-restraints excluded: chain H residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 160 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.182814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.146152 restraints weight = 15497.203| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.48 r_work: 0.3024 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15648 Z= 0.146 Angle : 0.519 5.485 21188 Z= 0.277 Chirality : 0.041 0.139 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.443 58.296 2128 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 0.99 (0.19), residues: 1876 helix: 1.65 (0.18), residues: 876 sheet: -0.29 (0.30), residues: 216 loop : -0.11 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 32 TYR 0.016 0.002 TYR C 147 PHE 0.022 0.001 PHE B 140 TRP 0.007 0.001 TRP D 436 HIS 0.001 0.000 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00345 (15644) covalent geometry : angle 0.51811 (21180) SS BOND : bond 0.00352 ( 4) SS BOND : angle 1.82434 ( 8) hydrogen bonds : bond 0.03975 ( 848) hydrogen bonds : angle 4.29134 ( 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 248 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 0.473 Fit side-chains REVERT: A 114 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7417 (mmt90) REVERT: A 186 PHE cc_start: 0.8043 (t80) cc_final: 0.7750 (t80) REVERT: A 319 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.7887 (p) REVERT: C 114 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7432 (mmt90) REVERT: C 186 PHE cc_start: 0.7977 (t80) cc_final: 0.7650 (t80) REVERT: C 319 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.7909 (p) REVERT: C 472 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 114 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7159 (mtp85) REVERT: B 146 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7053 (mt-10) REVERT: B 186 PHE cc_start: 0.7970 (t80) cc_final: 0.7650 (t80) REVERT: B 319 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.7918 (p) REVERT: D 114 ARG cc_start: 0.7739 (mmt-90) cc_final: 0.7521 (mmt90) REVERT: D 186 PHE cc_start: 0.7943 (t80) cc_final: 0.7616 (t80) REVERT: D 319 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.7922 (p) outliers start: 52 outliers final: 41 residues processed: 246 average time/residue: 0.1138 time to fit residues: 40.8189 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 : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 29 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 79 VAL 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 C residue 439 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 319 SER 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 429 SER Chi-restraints excluded: chain B residue 439 VAL 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 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 29 LEU 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 59 ASN Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.180410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139600 restraints weight = 15379.267| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.53 r_work: 0.3073 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15648 Z= 0.134 Angle : 0.514 5.450 21188 Z= 0.274 Chirality : 0.041 0.137 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.431 57.720 2128 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.22 % Allowed : 17.42 % 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: 0.99 (0.19), residues: 1876 helix: 1.68 (0.18), residues: 876 sheet: -0.35 (0.30), residues: 216 loop : -0.12 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.016 0.001 TYR A 163 PHE 0.017 0.001 PHE C 140 TRP 0.006 0.001 TRP C 436 HIS 0.001 0.000 HIS B 488 Details of bonding type rmsd covalent geometry : bond 0.00315 (15644) covalent geometry : angle 0.51284 (21180) SS BOND : bond 0.00297 ( 4) SS BOND : angle 1.66959 ( 8) hydrogen bonds : bond 0.03899 ( 848) hydrogen bonds : angle 4.28767 ( 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 249 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.890 Fit side-chains REVERT: A 114 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7380 (mmt90) REVERT: A 186 PHE cc_start: 0.8085 (t80) cc_final: 0.7833 (t80) REVERT: A 319 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.7997 (p) REVERT: E 47 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: C 114 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7456 (mmt90) REVERT: C 186 PHE cc_start: 0.8023 (t80) cc_final: 0.7721 (t80) REVERT: C 319 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8001 (p) REVERT: B 114 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7171 (mtp85) REVERT: B 146 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7137 (mt-10) REVERT: B 186 PHE cc_start: 0.8007 (t80) cc_final: 0.7700 (t80) REVERT: B 319 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.7998 (p) REVERT: D 114 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7418 (mmt90) REVERT: D 186 PHE cc_start: 0.7998 (t80) cc_final: 0.7696 (t80) REVERT: D 198 ARG cc_start: 0.6754 (mmt180) cc_final: 0.6539 (mmt180) REVERT: D 319 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.7996 (p) REVERT: F 47 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: G 47 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7908 (mt-10) outliers start: 53 outliers final: 35 residues processed: 244 average time/residue: 0.1143 time to fit residues: 40.9838 Evaluate side-chains 232 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 319 SER 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 E residue 79 VAL 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 405 LEU Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain D residue 319 SER 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 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 59 ASN Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 171 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 135 optimal weight: 0.0020 chunk 17 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.180896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.138096 restraints weight = 15446.116| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.53 r_work: 0.3000 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15648 Z= 0.121 Angle : 0.510 7.445 21188 Z= 0.270 Chirality : 0.040 0.133 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.354 56.642 2128 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.43 % Allowed : 18.20 % 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: 1.10 (0.19), residues: 1876 helix: 1.79 (0.18), residues: 876 sheet: -0.31 (0.30), residues: 216 loop : -0.08 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.016 0.001 TYR A 163 PHE 0.018 0.001 PHE B 140 TRP 0.005 0.001 TRP A 436 HIS 0.001 0.000 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00279 (15644) covalent geometry : angle 0.50930 (21180) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.52275 ( 8) hydrogen bonds : bond 0.03745 ( 848) hydrogen bonds : angle 4.23673 ( 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 239 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.502 Fit side-chains REVERT: A 114 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7428 (mmt90) REVERT: A 186 PHE cc_start: 0.8071 (t80) cc_final: 0.7793 (t80) REVERT: A 319 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.7971 (p) REVERT: A 420 GLU cc_start: 0.8445 (tt0) cc_final: 0.7837 (tt0) REVERT: C 114 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7227 (mtp85) REVERT: C 186 PHE cc_start: 0.7995 (t80) cc_final: 0.7685 (t80) REVERT: C 319 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.7988 (p) REVERT: C 420 GLU cc_start: 0.8450 (tt0) cc_final: 0.7839 (tt0) REVERT: B 114 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7130 (mtp85) REVERT: B 146 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 186 PHE cc_start: 0.7972 (t80) cc_final: 0.7657 (t80) REVERT: B 319 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.7971 (p) REVERT: B 420 GLU cc_start: 0.8448 (tt0) cc_final: 0.7838 (tt0) REVERT: D 114 ARG cc_start: 0.7707 (mmt-90) cc_final: 0.7476 (mmt90) REVERT: D 186 PHE cc_start: 0.7965 (t80) cc_final: 0.7653 (t80) REVERT: D 319 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.7961 (p) REVERT: D 420 GLU cc_start: 0.8449 (tt0) cc_final: 0.7832 (tt0) REVERT: F 47 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: G 47 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: H 47 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7833 (mt-10) outliers start: 40 outliers final: 31 residues processed: 237 average time/residue: 0.1178 time to fit residues: 41.3016 Evaluate side-chains 235 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 ASN Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 VAL 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 D residue 410 ILE 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 Chi-restraints excluded: chain H residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 44 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 167 optimal weight: 0.0060 chunk 139 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 170 optimal weight: 0.0170 chunk 183 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.181794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.140082 restraints weight = 15336.903| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.50 r_work: 0.3056 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15648 Z= 0.111 Angle : 0.502 6.648 21188 Z= 0.265 Chirality : 0.040 0.129 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.257 55.132 2128 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.49 % Allowed : 18.57 % Favored : 78.94 % 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 (0.19), residues: 1876 helix: 1.83 (0.18), residues: 892 sheet: -0.21 (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 A 170 TYR 0.015 0.001 TYR A 163 PHE 0.014 0.001 PHE D 148 TRP 0.005 0.001 TRP A 436 HIS 0.001 0.000 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00253 (15644) covalent geometry : angle 0.50141 (21180) SS BOND : bond 0.00199 ( 4) SS BOND : angle 1.35330 ( 8) hydrogen bonds : bond 0.03615 ( 848) hydrogen bonds : angle 4.20080 ( 2388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4423.25 seconds wall clock time: 76 minutes 16.99 seconds (4576.99 seconds total)