Starting phenix.real_space_refine on Fri Jul 3 19:12:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cty_45922/07_2026/9cty_45922.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cty_45922/07_2026/9cty_45922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cty_45922/07_2026/9cty_45922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cty_45922/07_2026/9cty_45922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cty_45922/07_2026/9cty_45922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cty_45922/07_2026/9cty_45922.map" } resolution = 3.03 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= 0.038 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 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15280 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "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: "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: "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: "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: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 2.90, per 1000 atoms: 0.19 Number of scatterers: 15280 At special positions: 0 Unit cell: (121.275, 121.275, 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=2.00 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.00 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.00 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.00 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: 1.12 Conformation dependent library (CDL) restraints added in 667.2 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 52.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.655A pdb=" N ILE A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.845A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 231 through 255 removed outlier: 4.264A pdb=" N THR A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 315 Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.864A pdb=" N ASP A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 349 removed outlier: 3.690A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 369 removed outlier: 4.176A pdb=" N ARG A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.539A 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 394 through 420 Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.368A pdb=" N TRP A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 474 Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.546A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 33 removed outlier: 3.516A pdb=" N ASN E 33 " --> pdb=" O PHE E 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 removed outlier: 3.516A pdb=" N ASN F 33 " --> pdb=" O PHE F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 33 removed outlier: 3.516A pdb=" N ASN G 33 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.516A pdb=" N ASN H 33 " --> pdb=" O PHE H 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.655A pdb=" N ILE B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.846A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 231 through 255 removed outlier: 4.264A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.864A pdb=" N ASP B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 3.691A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 369 removed outlier: 4.176A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.539A 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 394 through 420 Processing helix chain 'B' and resid 430 through 443 removed outlier: 4.368A pdb=" N TRP B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 474 Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.546A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.656A pdb=" N ILE C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.844A pdb=" N MET C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 225 Processing helix chain 'C' and resid 231 through 255 removed outlier: 4.264A pdb=" N THR C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 315 Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.864A pdb=" N ASP C 332 " --> pdb=" O MET C 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 3.691A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 369 removed outlier: 4.176A pdb=" N ARG C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.539A 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 394 through 420 Processing helix chain 'C' and resid 430 through 443 removed outlier: 4.368A pdb=" N TRP C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 474 Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.546A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.655A pdb=" N ILE D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.844A pdb=" N MET D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 231 through 255 removed outlier: 4.264A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 315 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.864A pdb=" N ASP D 332 " --> pdb=" O MET D 328 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 349 removed outlier: 3.690A pdb=" N PHE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 369 removed outlier: 4.177A pdb=" N ARG D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.539A 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 394 through 420 Processing helix chain 'D' and resid 430 through 443 removed outlier: 4.369A pdb=" N TRP D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 474 Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.545A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 9.042A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 146 " --> pdb=" O ASP A 141 " (cutoff:3.500A) 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 58 through 60 removed outlier: 6.706A pdb=" N TRP E 37 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA E 35 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.706A pdb=" N TRP E 37 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA E 35 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 8 Processing sheet with id=AA6, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.705A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG F 51 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA F 35 " --> pdb=" O ARG F 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.705A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG F 51 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA F 35 " --> pdb=" O ARG F 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 8 Processing sheet with id=AA9, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.706A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG G 51 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA G 35 " --> pdb=" O ARG G 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.706A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG G 51 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA G 35 " --> pdb=" O ARG G 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.706A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG H 51 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA H 35 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.706A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG H 51 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA H 35 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 113 through 118 removed outlier: 9.041A pdb=" N TYR B 147 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL B 107 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE B 149 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN B 109 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 146 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 113 through 118 removed outlier: 9.042A pdb=" N TYR C 147 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C 107 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 146 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 113 through 118 removed outlier: 9.041A pdb=" N TYR D 147 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL D 107 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE D 149 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 146 " --> pdb=" O ASP D 141 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2448 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: 2.22 Time building geometry restraints manager: 1.54 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: 3413 1.33 - 1.45: 3827 1.45 - 1.57: 8312 1.57 - 1.69: 0 1.69 - 1.82: 92 Bond restraints: 15644 Sorted by residual: bond pdb=" N ILE H 58 " pdb=" CA ILE H 58 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" N ILE G 58 " pdb=" CA ILE G 58 " ideal model delta sigma weight residual 1.460 1.501 -0.042 1.10e-02 8.26e+03 1.45e+01 bond pdb=" N ILE F 58 " pdb=" CA ILE F 58 " ideal model delta sigma weight residual 1.460 1.501 -0.042 1.10e-02 8.26e+03 1.45e+01 bond pdb=" N ILE E 58 " pdb=" CA ILE E 58 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.10e-02 8.26e+03 1.42e+01 bond pdb=" N ILE D 336 " pdb=" CA ILE D 336 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 15639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 19349 1.89 - 3.77: 1637 3.77 - 5.66: 166 5.66 - 7.55: 24 7.55 - 9.43: 4 Bond angle restraints: 21180 Sorted by residual: angle pdb=" CA GLY G 11 " pdb=" C GLY G 11 " pdb=" O GLY G 11 " ideal model delta sigma weight residual 122.33 118.35 3.98 8.10e-01 1.52e+00 2.41e+01 angle pdb=" CA GLY H 11 " pdb=" C GLY H 11 " pdb=" O GLY H 11 " ideal model delta sigma weight residual 122.33 118.35 3.98 8.10e-01 1.52e+00 2.41e+01 angle pdb=" CA GLY F 11 " pdb=" C GLY F 11 " pdb=" O GLY F 11 " ideal model delta sigma weight residual 122.33 118.38 3.95 8.10e-01 1.52e+00 2.38e+01 angle pdb=" CA GLY E 11 " pdb=" C GLY E 11 " pdb=" O GLY E 11 " ideal model delta sigma weight residual 122.33 118.42 3.91 8.10e-01 1.52e+00 2.33e+01 angle pdb=" N ASN F 84 " pdb=" CA ASN F 84 " pdb=" C ASN F 84 " ideal model delta sigma weight residual 112.93 106.83 6.10 1.33e+00 5.65e-01 2.10e+01 ... (remaining 21175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.61: 8050 12.61 - 25.22: 846 25.22 - 37.83: 240 37.83 - 50.44: 60 50.44 - 63.05: 28 Dihedral angle restraints: 9224 sinusoidal: 3732 harmonic: 5492 Sorted by residual: dihedral pdb=" C ASN F 33 " pdb=" N ASN F 33 " pdb=" CA ASN F 33 " pdb=" CB ASN F 33 " ideal model delta harmonic sigma weight residual -122.60 -112.46 -10.14 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" C ASN E 33 " pdb=" N ASN E 33 " pdb=" CA ASN E 33 " pdb=" CB ASN E 33 " ideal model delta harmonic sigma weight residual -122.60 -112.52 -10.08 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" C ASN H 33 " pdb=" N ASN H 33 " pdb=" CA ASN H 33 " pdb=" CB ASN H 33 " ideal model delta harmonic sigma weight residual -122.60 -112.55 -10.05 0 2.50e+00 1.60e-01 1.62e+01 ... (remaining 9221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1645 0.070 - 0.139: 556 0.139 - 0.209: 98 0.209 - 0.278: 21 0.278 - 0.348: 12 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CB VAL E 13 " pdb=" CA VAL E 13 " pdb=" CG1 VAL E 13 " pdb=" CG2 VAL E 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB VAL H 13 " pdb=" CA VAL H 13 " pdb=" CG1 VAL H 13 " pdb=" CG2 VAL H 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL G 13 " pdb=" CA VAL G 13 " pdb=" CG1 VAL G 13 " pdb=" CG2 VAL G 13 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2329 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 135 " -0.258 9.50e-02 1.11e+02 1.16e-01 8.38e+00 pdb=" NE ARG C 135 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 135 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 135 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 135 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 135 " 0.257 9.50e-02 1.11e+02 1.15e-01 8.33e+00 pdb=" NE ARG B 135 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 135 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 135 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 135 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 135 " -0.258 9.50e-02 1.11e+02 1.16e-01 8.33e+00 pdb=" NE ARG D 135 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 135 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 135 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 135 " -0.011 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.91: 6309 2.91 - 3.47: 17055 3.47 - 4.03: 28229 4.03 - 4.58: 40958 4.58 - 5.14: 58532 Nonbonded interactions: 151083 Sorted by model distance: nonbonded pdb=" OD1 ASN F 33 " pdb=" OH TYR F 104 " model vdw 2.358 3.040 nonbonded pdb=" OD1 ASN H 33 " pdb=" OH TYR H 104 " model vdw 2.359 3.040 nonbonded pdb=" OD1 ASN E 33 " pdb=" OH TYR E 104 " model vdw 2.359 3.040 nonbonded pdb=" OD1 ASN G 33 " pdb=" OH TYR G 104 " model vdw 2.359 3.040 nonbonded pdb=" O LEU H 29 " pdb=" ND2 ASN H 33 " model vdw 2.363 3.120 ... (remaining 151078 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: 5.320 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.740 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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: 19.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.011 0.090 15648 Z= 0.617 Angle : 1.116 9.433 21188 Z= 0.714 Chirality : 0.073 0.348 2332 Planarity : 0.012 0.116 2700 Dihedral : 12.150 63.052 5692 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.43 % Allowed : 7.83 % Favored : 89.75 % 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: -1.01 (0.19), residues: 1876 helix: -0.15 (0.17), residues: 896 sheet: -0.60 (0.35), residues: 220 loop : -1.19 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.003 ARG F 72 TYR 0.028 0.006 TYR G 106 PHE 0.033 0.006 PHE D 406 TRP 0.027 0.006 TRP A 305 HIS 0.017 0.009 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.01113 / 0.62 (15644) covalent geometry : angle 1.11592 / 0.71 (21180) SS BOND : bond 0.03348 / 2.03 ( 4) SS BOND : angle 1.96379 / 1.15 ( 8) hydrogen bonds : bond 0.14427 / 9.76 ( 816) hydrogen bonds : angle 6.37220 / 4.37 ( 2448) *********************** 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 339 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.540 Fit side-chains REVERT: A 107 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 114 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7458 (tpp80) REVERT: A 137 MET cc_start: 0.7514 (mmm) cc_final: 0.7289 (tpt) REVERT: A 140 PHE cc_start: 0.7547 (t80) cc_final: 0.7319 (t80) REVERT: A 141 ASP cc_start: 0.6970 (t70) cc_final: 0.6350 (t0) REVERT: A 156 PHE cc_start: 0.8635 (t80) cc_final: 0.8375 (t80) REVERT: A 170 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8167 (mtt90) REVERT: A 205 ARG cc_start: 0.4844 (OUTLIER) cc_final: 0.4411 (mtp180) REVERT: A 247 SER cc_start: 0.8679 (t) cc_final: 0.8472 (p) REVERT: A 328 MET cc_start: 0.8482 (mtm) cc_final: 0.8260 (mtp) REVERT: E 22 SER cc_start: 0.7564 (t) cc_final: 0.7356 (p) REVERT: E 57 SER cc_start: 0.6693 (t) cc_final: 0.6477 (m) REVERT: E 83 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.4666 (mpp) REVERT: G 73 ASP cc_start: 0.6935 (m-30) cc_final: 0.6254 (t70) REVERT: H 22 SER cc_start: 0.7654 (t) cc_final: 0.7327 (p) REVERT: H 83 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.4370 (mpp) REVERT: B 114 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7494 (ttm110) REVERT: B 137 MET cc_start: 0.7638 (mmm) cc_final: 0.7373 (tpt) REVERT: B 141 ASP cc_start: 0.7016 (t70) cc_final: 0.6450 (t0) REVERT: B 170 ARG cc_start: 0.8612 (mtt180) cc_final: 0.8203 (mtt90) REVERT: B 205 ARG cc_start: 0.5183 (OUTLIER) cc_final: 0.4633 (mtp180) REVERT: B 365 VAL cc_start: 0.7980 (p) cc_final: 0.7661 (m) REVERT: B 449 ASP cc_start: 0.8708 (p0) cc_final: 0.8423 (p0) REVERT: C 114 ARG cc_start: 0.8303 (ttm170) cc_final: 0.7581 (ttm110) REVERT: C 137 MET cc_start: 0.7570 (mmm) cc_final: 0.7292 (mmm) REVERT: C 141 ASP cc_start: 0.6983 (t70) cc_final: 0.6388 (t0) REVERT: C 170 ARG cc_start: 0.8550 (mtt180) cc_final: 0.8160 (mtt90) REVERT: C 205 ARG cc_start: 0.4881 (OUTLIER) cc_final: 0.4456 (mtp180) REVERT: C 247 SER cc_start: 0.8646 (t) cc_final: 0.8404 (p) REVERT: D 114 ARG cc_start: 0.8303 (ttm170) cc_final: 0.7523 (ttm110) REVERT: D 137 MET cc_start: 0.7575 (mmm) cc_final: 0.7310 (tpt) REVERT: D 140 PHE cc_start: 0.7405 (t80) cc_final: 0.7200 (t80) REVERT: D 141 ASP cc_start: 0.6910 (t70) cc_final: 0.6333 (t0) REVERT: D 156 PHE cc_start: 0.8572 (t80) cc_final: 0.8345 (t80) REVERT: D 170 ARG cc_start: 0.8586 (mtt180) cc_final: 0.8245 (mtt90) REVERT: D 205 ARG cc_start: 0.4966 (OUTLIER) cc_final: 0.4554 (mtp180) REVERT: D 247 SER cc_start: 0.8678 (t) cc_final: 0.8467 (p) REVERT: D 328 MET cc_start: 0.8460 (mtm) cc_final: 0.8185 (mtp) REVERT: D 365 VAL cc_start: 0.7871 (p) cc_final: 0.7604 (m) outliers start: 40 outliers final: 12 residues processed: 327 average time/residue: 0.1261 time to fit residues: 58.2630 Evaluate side-chains 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 205 ARG Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 124 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN E 4 GLN F 4 GLN G 4 GLN H 4 GLN B 109 ASN B 124 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN C 109 ASN C 124 GLN C 482 ASN D 109 ASN D 124 GLN D 329 ASN D 482 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.209085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143399 restraints weight = 15187.162| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.77 r_work: 0.3087 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15648 Z= 0.142 Angle : 0.534 5.426 21188 Z= 0.283 Chirality : 0.041 0.119 2332 Planarity : 0.005 0.042 2700 Dihedral : 6.002 56.067 2175 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.55 % Allowed : 11.29 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.21), residues: 1876 helix: 1.02 (0.18), residues: 880 sheet: -0.02 (0.37), residues: 212 loop : -0.10 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 144 TYR 0.016 0.001 TYR F 94 PHE 0.020 0.001 PHE A 197 TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15644) covalent geometry : angle 0.53427 / 0.28 (21180) SS BOND : bond 0.00160 / 0.10 ( 4) SS BOND : angle 0.92067 / 0.48 ( 8) hydrogen bonds : bond 0.04029 / 2.68 ( 816) hydrogen bonds : angle 4.63373 / 3.19 ( 2448) *********************** 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 252 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.536 Fit side-chains REVERT: A 114 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7631 (mmt180) REVERT: A 141 ASP cc_start: 0.7214 (t70) cc_final: 0.6641 (t0) REVERT: A 194 MET cc_start: 0.6930 (tpp) cc_final: 0.6679 (mmt) REVERT: A 205 ARG cc_start: 0.5133 (OUTLIER) cc_final: 0.4673 (mtp180) REVERT: A 389 GLN cc_start: 0.8997 (mt0) cc_final: 0.8791 (mt0) REVERT: E 73 ASP cc_start: 0.7214 (m-30) cc_final: 0.6588 (t70) REVERT: F 73 ASP cc_start: 0.7161 (m-30) cc_final: 0.6547 (t70) REVERT: G 73 ASP cc_start: 0.7291 (m-30) cc_final: 0.6791 (t70) REVERT: H 22 SER cc_start: 0.7724 (t) cc_final: 0.7516 (p) REVERT: B 114 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7576 (ttm-80) REVERT: B 137 MET cc_start: 0.7779 (mmm) cc_final: 0.7530 (tpt) REVERT: B 140 PHE cc_start: 0.8114 (t80) cc_final: 0.7856 (t80) REVERT: B 141 ASP cc_start: 0.7149 (t70) cc_final: 0.6646 (t0) REVERT: B 205 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4858 (mtp180) REVERT: B 365 VAL cc_start: 0.8109 (p) cc_final: 0.7854 (m) REVERT: B 389 GLN cc_start: 0.8972 (mt0) cc_final: 0.8769 (mt0) REVERT: C 114 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7658 (ttm170) REVERT: C 137 MET cc_start: 0.7652 (mmm) cc_final: 0.7292 (mmm) REVERT: C 141 ASP cc_start: 0.7211 (t70) cc_final: 0.6673 (t0) REVERT: C 194 MET cc_start: 0.6992 (tpp) cc_final: 0.6625 (mmt) REVERT: C 205 ARG cc_start: 0.5111 (OUTLIER) cc_final: 0.4684 (mtp180) REVERT: C 389 GLN cc_start: 0.8999 (mt0) cc_final: 0.8795 (mt0) REVERT: D 114 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7547 (mmt180) REVERT: D 137 MET cc_start: 0.7742 (mmm) cc_final: 0.7484 (tpt) REVERT: D 141 ASP cc_start: 0.7119 (t70) cc_final: 0.6588 (t0) REVERT: D 205 ARG cc_start: 0.5218 (OUTLIER) cc_final: 0.4743 (mtp180) outliers start: 42 outliers final: 21 residues processed: 235 average time/residue: 0.1230 time to fit residues: 41.4354 Evaluate side-chains 204 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 205 ARG Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 92 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN B 329 ASN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.208177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141528 restraints weight = 15309.951| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.12 r_work: 0.3193 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15648 Z= 0.143 Angle : 0.507 5.534 21188 Z= 0.270 Chirality : 0.041 0.121 2332 Planarity : 0.005 0.045 2700 Dihedral : 5.589 51.967 2168 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.85 % Allowed : 12.68 % Favored : 84.47 % 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 (0.21), residues: 1876 helix: 1.34 (0.18), residues: 888 sheet: 0.20 (0.37), residues: 212 loop : 0.22 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.013 0.001 TYR G 94 PHE 0.012 0.001 PHE C 197 TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (15644) covalent geometry : angle 0.50655 / 0.27 (21180) SS BOND : bond 0.00136 / 0.08 ( 4) SS BOND : angle 0.98719 / 0.53 ( 8) hydrogen bonds : bond 0.03814 / 2.55 ( 816) hydrogen bonds : angle 4.32591 / 2.99 ( 2448) *********************** 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 237 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 190 time to evaluate : 0.489 Fit side-chains REVERT: A 114 ARG cc_start: 0.8323 (ttm170) cc_final: 0.7616 (mmt180) REVERT: A 137 MET cc_start: 0.7879 (tpt) cc_final: 0.7538 (mmm) REVERT: A 141 ASP cc_start: 0.7196 (t70) cc_final: 0.6652 (t0) REVERT: A 194 MET cc_start: 0.6999 (tpp) cc_final: 0.6759 (mmt) REVERT: A 205 ARG cc_start: 0.5091 (OUTLIER) cc_final: 0.4641 (mtp180) REVERT: E 73 ASP cc_start: 0.7266 (m-30) cc_final: 0.6577 (t70) REVERT: E 83 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.5336 (mmm) REVERT: F 73 ASP cc_start: 0.7194 (m-30) cc_final: 0.6506 (t70) REVERT: G 73 ASP cc_start: 0.7261 (m-30) cc_final: 0.6680 (t70) REVERT: H 22 SER cc_start: 0.7709 (t) cc_final: 0.7445 (p) REVERT: H 83 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.5402 (mmm) REVERT: B 114 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7628 (ttm170) REVERT: B 137 MET cc_start: 0.7829 (mmm) cc_final: 0.7587 (tpt) REVERT: B 141 ASP cc_start: 0.7204 (t70) cc_final: 0.6653 (t0) REVERT: B 205 ARG cc_start: 0.5317 (OUTLIER) cc_final: 0.4778 (mtp180) REVERT: B 247 SER cc_start: 0.8800 (t) cc_final: 0.8488 (p) REVERT: C 114 ARG cc_start: 0.8286 (ttm170) cc_final: 0.7725 (ttm170) REVERT: C 137 MET cc_start: 0.7655 (mmm) cc_final: 0.7433 (mmp) REVERT: C 141 ASP cc_start: 0.7220 (t70) cc_final: 0.6681 (t0) REVERT: C 170 ARG cc_start: 0.8598 (mtt90) cc_final: 0.8145 (mtt90) REVERT: C 205 ARG cc_start: 0.5087 (OUTLIER) cc_final: 0.4656 (mtp180) REVERT: D 114 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7639 (mmt180) REVERT: D 140 PHE cc_start: 0.8336 (t80) cc_final: 0.7993 (t80) REVERT: D 141 ASP cc_start: 0.7193 (t70) cc_final: 0.6780 (t0) REVERT: D 205 ARG cc_start: 0.5193 (OUTLIER) cc_final: 0.4709 (mtp180) outliers start: 47 outliers final: 20 residues processed: 220 average time/residue: 0.1191 time to fit residues: 38.2413 Evaluate side-chains 198 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 205 ARG Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 6 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN D 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.205569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137329 restraints weight = 15303.249| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.44 r_work: 0.3102 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15648 Z= 0.203 Angle : 0.544 5.668 21188 Z= 0.288 Chirality : 0.043 0.128 2332 Planarity : 0.005 0.049 2700 Dihedral : 5.297 52.676 2152 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.67 % Allowed : 14.32 % Favored : 83.01 % 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: 1.05 (0.21), residues: 1876 helix: 1.28 (0.18), residues: 884 sheet: 0.32 (0.37), residues: 212 loop : 0.29 (0.25), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.012 0.001 TYR G 106 PHE 0.019 0.001 PHE D 197 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.20 (15644) covalent geometry : angle 0.54303 / 0.29 (21180) SS BOND : bond 0.00238 / 0.14 ( 4) SS BOND : angle 1.41949 / 0.76 ( 8) hydrogen bonds : bond 0.04147 / 2.75 ( 816) hydrogen bonds : angle 4.33336 / 3.00 ( 2448) *********************** 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 225 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.408 Fit side-chains REVERT: A 114 ARG cc_start: 0.8345 (ttm170) cc_final: 0.7628 (mmt180) REVERT: A 137 MET cc_start: 0.7933 (tpt) cc_final: 0.7630 (mmm) REVERT: A 141 ASP cc_start: 0.7170 (t70) cc_final: 0.6714 (t0) REVERT: A 194 MET cc_start: 0.6919 (tpp) cc_final: 0.6518 (mmt) REVERT: A 205 ARG cc_start: 0.5070 (OUTLIER) cc_final: 0.4588 (mtp180) REVERT: E 73 ASP cc_start: 0.7306 (m-30) cc_final: 0.6621 (t70) REVERT: E 83 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.5402 (mmm) REVERT: F 33 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8319 (m-40) REVERT: F 73 ASP cc_start: 0.7252 (m-30) cc_final: 0.6606 (t70) REVERT: G 73 ASP cc_start: 0.7296 (m-30) cc_final: 0.6695 (t70) REVERT: H 22 SER cc_start: 0.7869 (t) cc_final: 0.7553 (p) REVERT: H 73 ASP cc_start: 0.7257 (m-30) cc_final: 0.6525 (t70) REVERT: H 83 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.5378 (mmm) REVERT: B 114 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7630 (tpp80) REVERT: B 137 MET cc_start: 0.7840 (mmm) cc_final: 0.7638 (tpt) REVERT: B 141 ASP cc_start: 0.7169 (t70) cc_final: 0.6640 (t0) REVERT: B 205 ARG cc_start: 0.5321 (OUTLIER) cc_final: 0.4754 (mtp180) REVERT: B 247 SER cc_start: 0.8873 (t) cc_final: 0.8510 (p) REVERT: C 114 ARG cc_start: 0.8324 (ttm170) cc_final: 0.7688 (ttm-80) REVERT: C 137 MET cc_start: 0.7683 (mmm) cc_final: 0.7430 (mmp) REVERT: C 141 ASP cc_start: 0.7171 (t70) cc_final: 0.6687 (t0) REVERT: C 170 ARG cc_start: 0.8701 (mtt90) cc_final: 0.8105 (mtt90) REVERT: C 205 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.4588 (mtp180) REVERT: D 114 ARG cc_start: 0.8371 (ttm170) cc_final: 0.7690 (tpp80) REVERT: D 137 MET cc_start: 0.7948 (tpt) cc_final: 0.7697 (mmm) REVERT: D 141 ASP cc_start: 0.7161 (t70) cc_final: 0.6732 (t0) REVERT: D 205 ARG cc_start: 0.5181 (OUTLIER) cc_final: 0.4659 (mtp180) outliers start: 44 outliers final: 22 residues processed: 210 average time/residue: 0.1271 time to fit residues: 38.8294 Evaluate side-chains 203 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 205 ARG Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 185 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.208508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145319 restraints weight = 15335.771| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.81 r_work: 0.3103 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15648 Z= 0.113 Angle : 0.481 5.556 21188 Z= 0.254 Chirality : 0.040 0.121 2332 Planarity : 0.004 0.046 2700 Dihedral : 5.061 52.615 2152 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.43 % Allowed : 14.50 % Favored : 83.07 % 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: 1.30 (0.21), residues: 1876 helix: 1.49 (0.18), residues: 892 sheet: 0.69 (0.37), residues: 212 loop : 0.30 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 100 TYR 0.010 0.001 TYR B 161 PHE 0.019 0.001 PHE C 197 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (15644) covalent geometry : angle 0.48033 / 0.25 (21180) SS BOND : bond 0.00030 / 0.02 ( 4) SS BOND : angle 0.86828 / 0.47 ( 8) hydrogen bonds : bond 0.03420 / 2.26 ( 816) hydrogen bonds : angle 4.02329 / 2.79 ( 2448) *********************** 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 227 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.602 Fit side-chains REVERT: A 114 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7815 (mpt180) REVERT: A 137 MET cc_start: 0.7918 (tpt) cc_final: 0.7676 (mmm) REVERT: A 141 ASP cc_start: 0.7245 (t70) cc_final: 0.6866 (t0) REVERT: A 194 MET cc_start: 0.7053 (tpp) cc_final: 0.6831 (mmt) REVERT: A 205 ARG cc_start: 0.5127 (OUTLIER) cc_final: 0.4650 (mtp180) REVERT: E 73 ASP cc_start: 0.7320 (m-30) cc_final: 0.6736 (t70) REVERT: E 83 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.5470 (mmm) REVERT: E 104 TYR cc_start: 0.8827 (p90) cc_final: 0.8617 (p90) REVERT: F 73 ASP cc_start: 0.7303 (m-30) cc_final: 0.6739 (t70) REVERT: G 73 ASP cc_start: 0.7415 (m-30) cc_final: 0.6900 (t70) REVERT: H 22 SER cc_start: 0.7740 (t) cc_final: 0.7392 (p) REVERT: H 73 ASP cc_start: 0.7354 (m-30) cc_final: 0.6678 (t70) REVERT: H 83 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.5271 (mmm) REVERT: B 114 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7731 (tpp80) REVERT: B 141 ASP cc_start: 0.7174 (t70) cc_final: 0.6803 (t0) REVERT: B 205 ARG cc_start: 0.5271 (OUTLIER) cc_final: 0.4779 (mtp180) REVERT: B 247 SER cc_start: 0.8810 (t) cc_final: 0.8558 (p) REVERT: C 114 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7789 (mpt180) REVERT: C 137 MET cc_start: 0.7653 (mmm) cc_final: 0.7416 (mmp) REVERT: C 141 ASP cc_start: 0.7300 (t70) cc_final: 0.6899 (t0) REVERT: C 170 ARG cc_start: 0.8729 (mtt90) cc_final: 0.8175 (mtt90) REVERT: C 194 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6679 (mmt) REVERT: C 205 ARG cc_start: 0.5115 (OUTLIER) cc_final: 0.4639 (mtp180) REVERT: D 114 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7781 (mpt180) REVERT: D 137 MET cc_start: 0.7924 (tpt) cc_final: 0.7697 (mmm) REVERT: D 141 ASP cc_start: 0.7304 (t70) cc_final: 0.6942 (t0) REVERT: D 205 ARG cc_start: 0.5253 (OUTLIER) cc_final: 0.4739 (mtp180) outliers start: 40 outliers final: 17 residues processed: 218 average time/residue: 0.1270 time to fit residues: 40.4784 Evaluate side-chains 188 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 205 ARG Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 444 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 166 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 144 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.207514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142427 restraints weight = 15237.598| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.83 r_work: 0.3109 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15648 Z= 0.137 Angle : 0.497 5.773 21188 Z= 0.263 Chirality : 0.041 0.121 2332 Planarity : 0.004 0.047 2700 Dihedral : 5.054 52.897 2152 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.12 % Allowed : 15.47 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1876 helix: 1.57 (0.18), residues: 892 sheet: 0.77 (0.38), residues: 212 loop : 0.33 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 100 TYR 0.008 0.001 TYR A 161 PHE 0.017 0.001 PHE A 140 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (15644) covalent geometry : angle 0.49640 / 0.26 (21180) SS BOND : bond 0.00112 / 0.06 ( 4) SS BOND : angle 1.09228 / 0.59 ( 8) hydrogen bonds : bond 0.03606 / 2.39 ( 816) hydrogen bonds : angle 3.94310 / 2.74 ( 2448) *********************** 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 217 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.553 Fit side-chains REVERT: A 114 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7788 (mpt180) REVERT: A 137 MET cc_start: 0.7896 (tpt) cc_final: 0.7653 (mmm) REVERT: A 141 ASP cc_start: 0.7183 (t70) cc_final: 0.6822 (t0) REVERT: A 194 MET cc_start: 0.7012 (tpp) cc_final: 0.6763 (mmt) REVERT: A 205 ARG cc_start: 0.5137 (OUTLIER) cc_final: 0.4656 (mtp180) REVERT: E 73 ASP cc_start: 0.7356 (m-30) cc_final: 0.6820 (t70) REVERT: E 83 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.5493 (mmm) REVERT: F 73 ASP cc_start: 0.7333 (m-30) cc_final: 0.6800 (t70) REVERT: G 73 ASP cc_start: 0.7258 (m-30) cc_final: 0.6919 (t70) REVERT: H 22 SER cc_start: 0.7763 (t) cc_final: 0.7438 (p) REVERT: H 73 ASP cc_start: 0.7332 (m-30) cc_final: 0.6677 (t70) REVERT: H 83 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.5320 (mmm) REVERT: B 114 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7684 (tpp80) REVERT: B 141 ASP cc_start: 0.7209 (t70) cc_final: 0.6806 (t0) REVERT: B 205 ARG cc_start: 0.5154 (OUTLIER) cc_final: 0.4696 (mtp180) REVERT: B 247 SER cc_start: 0.8834 (t) cc_final: 0.8577 (p) REVERT: C 114 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7770 (mpt180) REVERT: C 137 MET cc_start: 0.7685 (mmm) cc_final: 0.7439 (mmp) REVERT: C 141 ASP cc_start: 0.7196 (t70) cc_final: 0.6843 (t0) REVERT: C 170 ARG cc_start: 0.8771 (mtt90) cc_final: 0.8149 (mtt90) REVERT: C 205 ARG cc_start: 0.5093 (OUTLIER) cc_final: 0.4648 (mtp180) REVERT: D 114 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7746 (mpt180) REVERT: D 141 ASP cc_start: 0.7215 (t70) cc_final: 0.6834 (t0) REVERT: D 205 ARG cc_start: 0.5135 (OUTLIER) cc_final: 0.4650 (mtp180) outliers start: 35 outliers final: 20 residues processed: 208 average time/residue: 0.1344 time to fit residues: 40.4035 Evaluate side-chains 194 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 205 ARG Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 444 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 106 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 ASN F 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.206856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140516 restraints weight = 15111.098| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.22 r_work: 0.3154 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15648 Z= 0.160 Angle : 0.513 6.140 21188 Z= 0.271 Chirality : 0.041 0.124 2332 Planarity : 0.004 0.047 2700 Dihedral : 5.117 53.213 2152 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.06 % Allowed : 16.20 % Favored : 81.74 % 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: 1.29 (0.21), residues: 1876 helix: 1.53 (0.18), residues: 896 sheet: 0.53 (0.37), residues: 220 loop : 0.28 (0.26), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 100 TYR 0.015 0.001 TYR F 104 PHE 0.020 0.001 PHE C 197 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (15644) covalent geometry : angle 0.51225 / 0.27 (21180) SS BOND : bond 0.00131 / 0.08 ( 4) SS BOND : angle 1.18615 / 0.64 ( 8) hydrogen bonds : bond 0.03736 / 2.46 ( 816) hydrogen bonds : angle 3.90733 / 2.71 ( 2448) *********************** 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 212 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.495 Fit side-chains REVERT: A 114 ARG cc_start: 0.8261 (ttm170) cc_final: 0.7678 (mpt180) REVERT: A 137 MET cc_start: 0.7889 (tpt) cc_final: 0.7579 (mmm) REVERT: A 141 ASP cc_start: 0.7071 (t70) cc_final: 0.6691 (t0) REVERT: A 194 MET cc_start: 0.6910 (tpp) cc_final: 0.6587 (mmt) REVERT: A 205 ARG cc_start: 0.4983 (OUTLIER) cc_final: 0.4569 (mtp180) REVERT: E 73 ASP cc_start: 0.7278 (m-30) cc_final: 0.6654 (t70) REVERT: E 83 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.5296 (mmm) REVERT: F 73 ASP cc_start: 0.7230 (m-30) cc_final: 0.6611 (t70) REVERT: G 73 ASP cc_start: 0.7176 (m-30) cc_final: 0.6716 (t70) REVERT: H 22 SER cc_start: 0.7673 (t) cc_final: 0.7327 (p) REVERT: H 73 ASP cc_start: 0.7232 (m-30) cc_final: 0.6499 (t70) REVERT: H 83 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.5150 (mmm) REVERT: B 114 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7603 (tpp80) REVERT: B 141 ASP cc_start: 0.7044 (t70) cc_final: 0.6670 (t0) REVERT: B 205 ARG cc_start: 0.5004 (OUTLIER) cc_final: 0.4579 (mtp180) REVERT: B 247 SER cc_start: 0.8856 (t) cc_final: 0.8528 (p) REVERT: C 114 ARG cc_start: 0.8259 (ttm170) cc_final: 0.7695 (mpt180) REVERT: C 137 MET cc_start: 0.7715 (mmm) cc_final: 0.7467 (mmp) REVERT: C 141 ASP cc_start: 0.7040 (t70) cc_final: 0.6678 (t0) REVERT: C 205 ARG cc_start: 0.4954 (OUTLIER) cc_final: 0.4543 (mtp180) REVERT: D 114 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7660 (mpt180) REVERT: D 141 ASP cc_start: 0.7040 (t70) cc_final: 0.6675 (t0) REVERT: D 205 ARG cc_start: 0.5001 (OUTLIER) cc_final: 0.4793 (ptm160) REVERT: D 365 VAL cc_start: 0.8127 (p) cc_final: 0.7834 (m) outliers start: 34 outliers final: 20 residues processed: 201 average time/residue: 0.1266 time to fit residues: 36.8328 Evaluate side-chains 194 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 205 ARG Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 444 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 160 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 chunk 32 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 ASN F 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.207726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142632 restraints weight = 15333.322| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.83 r_work: 0.3111 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15648 Z= 0.131 Angle : 0.495 7.142 21188 Z= 0.261 Chirality : 0.040 0.120 2332 Planarity : 0.004 0.046 2700 Dihedral : 5.030 53.135 2152 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.06 % Allowed : 16.26 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1876 helix: 1.63 (0.18), residues: 900 sheet: 0.57 (0.37), residues: 220 loop : 0.30 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100 TYR 0.010 0.001 TYR E 104 PHE 0.019 0.001 PHE C 197 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS D 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (15644) covalent geometry : angle 0.49445 / 0.26 (21180) SS BOND : bond 0.00070 / 0.04 ( 4) SS BOND : angle 1.01906 / 0.55 ( 8) hydrogen bonds : bond 0.03523 / 2.32 ( 816) hydrogen bonds : angle 3.84845 / 2.67 ( 2448) *********************** 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 216 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.558 Fit side-chains REVERT: A 114 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7755 (mpt180) REVERT: A 137 MET cc_start: 0.7868 (tpt) cc_final: 0.7636 (mmm) REVERT: A 141 ASP cc_start: 0.7096 (t70) cc_final: 0.6781 (t0) REVERT: A 194 MET cc_start: 0.7031 (tpp) cc_final: 0.6726 (mmt) REVERT: A 205 ARG cc_start: 0.5130 (OUTLIER) cc_final: 0.4673 (mtp180) REVERT: E 73 ASP cc_start: 0.7349 (m-30) cc_final: 0.6817 (t70) REVERT: E 83 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.5468 (mmm) REVERT: F 73 ASP cc_start: 0.7335 (m-30) cc_final: 0.6807 (t70) REVERT: G 73 ASP cc_start: 0.7231 (m-30) cc_final: 0.6887 (t70) REVERT: H 22 SER cc_start: 0.7701 (t) cc_final: 0.7332 (p) REVERT: H 73 ASP cc_start: 0.7324 (m-30) cc_final: 0.6692 (t70) REVERT: H 83 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.5156 (mmm) REVERT: B 114 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7643 (tpp80) REVERT: B 137 MET cc_start: 0.8381 (mmp) cc_final: 0.7957 (tpt) REVERT: B 141 ASP cc_start: 0.7056 (t70) cc_final: 0.6761 (t0) REVERT: B 205 ARG cc_start: 0.5157 (OUTLIER) cc_final: 0.4681 (mtp180) REVERT: B 247 SER cc_start: 0.8794 (t) cc_final: 0.8529 (p) REVERT: C 114 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7757 (mpt180) REVERT: C 137 MET cc_start: 0.7688 (mmm) cc_final: 0.7445 (mmp) REVERT: C 141 ASP cc_start: 0.7090 (t70) cc_final: 0.6779 (t0) REVERT: D 114 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7716 (mpt180) REVERT: D 137 MET cc_start: 0.8241 (mmm) cc_final: 0.7604 (tpp) REVERT: D 140 PHE cc_start: 0.8614 (t80) cc_final: 0.8411 (t80) REVERT: D 141 ASP cc_start: 0.7016 (t70) cc_final: 0.6694 (t0) REVERT: D 205 ARG cc_start: 0.5140 (OUTLIER) cc_final: 0.4910 (ptm160) outliers start: 34 outliers final: 20 residues processed: 206 average time/residue: 0.1268 time to fit residues: 37.9347 Evaluate side-chains 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 444 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 118 optimal weight: 0.0050 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.208037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140413 restraints weight = 15254.066| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.90 r_work: 0.3107 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15648 Z= 0.131 Angle : 0.496 6.727 21188 Z= 0.262 Chirality : 0.040 0.119 2332 Planarity : 0.004 0.046 2700 Dihedral : 4.879 53.223 2148 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.64 % Allowed : 16.93 % Favored : 81.43 % 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: 1.44 (0.21), residues: 1876 helix: 1.68 (0.18), residues: 900 sheet: 0.59 (0.37), residues: 220 loop : 0.32 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 100 TYR 0.014 0.001 TYR F 104 PHE 0.018 0.001 PHE B 140 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (15644) covalent geometry : angle 0.49565 / 0.26 (21180) SS BOND : bond 0.00065 / 0.04 ( 4) SS BOND : angle 1.01320 / 0.54 ( 8) hydrogen bonds : bond 0.03491 / 2.29 ( 816) hydrogen bonds : angle 3.82475 / 2.65 ( 2448) *********************** 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 208 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.475 Fit side-chains REVERT: A 114 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7602 (mpt180) REVERT: A 137 MET cc_start: 0.7833 (tpt) cc_final: 0.7602 (mmm) REVERT: A 141 ASP cc_start: 0.6984 (t70) cc_final: 0.6689 (t0) REVERT: A 194 MET cc_start: 0.7021 (tpp) cc_final: 0.6677 (mmt) REVERT: E 73 ASP cc_start: 0.7286 (m-30) cc_final: 0.6711 (t70) REVERT: E 83 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.5326 (mmm) REVERT: F 73 ASP cc_start: 0.7270 (m-30) cc_final: 0.6708 (t70) REVERT: G 73 ASP cc_start: 0.7115 (m-30) cc_final: 0.6744 (t70) REVERT: H 22 SER cc_start: 0.7638 (t) cc_final: 0.7248 (p) REVERT: H 73 ASP cc_start: 0.7217 (m-30) cc_final: 0.6548 (t70) REVERT: H 83 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.5155 (mmm) REVERT: B 114 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7502 (tpp80) REVERT: B 137 MET cc_start: 0.8343 (mmp) cc_final: 0.7918 (tpt) REVERT: B 141 ASP cc_start: 0.6959 (t70) cc_final: 0.6673 (t0) REVERT: B 205 ARG cc_start: 0.5119 (OUTLIER) cc_final: 0.4919 (ptm160) REVERT: B 247 SER cc_start: 0.8722 (t) cc_final: 0.8431 (p) REVERT: C 114 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7549 (tpp80) REVERT: C 137 MET cc_start: 0.7678 (mmm) cc_final: 0.7444 (mmp) REVERT: C 141 ASP cc_start: 0.7036 (t70) cc_final: 0.6717 (t0) REVERT: D 114 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7556 (mpt180) REVERT: D 141 ASP cc_start: 0.6993 (t70) cc_final: 0.6687 (t0) outliers start: 27 outliers final: 20 residues processed: 198 average time/residue: 0.1311 time to fit residues: 37.5496 Evaluate side-chains 203 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 444 THR 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: 0.4980 chunk 22 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 176 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.209465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127309 restraints weight = 15242.670| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.11 r_work: 0.3161 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2909 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= 0.111 Angle : 0.485 6.734 21188 Z= 0.257 Chirality : 0.040 0.118 2332 Planarity : 0.004 0.046 2700 Dihedral : 4.509 52.911 2140 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.64 % Allowed : 16.87 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1876 helix: 1.83 (0.18), residues: 900 sheet: 0.49 (0.37), residues: 220 loop : 0.34 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 170 TYR 0.013 0.001 TYR E 104 PHE 0.017 0.001 PHE A 140 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (15644) covalent geometry : angle 0.48517 / 0.26 (21180) SS BOND : bond 0.00011 / 0.01 ( 4) SS BOND : angle 0.87851 / 0.47 ( 8) hydrogen bonds : bond 0.03281 / 2.16 ( 816) hydrogen bonds : angle 3.76257 / 2.60 ( 2448) ********************** 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 213 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.566 Fit side-chains REVERT: A 114 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7477 (tpp80) REVERT: A 137 MET cc_start: 0.7876 (tpt) cc_final: 0.7565 (mmm) REVERT: A 141 ASP cc_start: 0.6898 (t70) cc_final: 0.6602 (t0) REVERT: A 194 MET cc_start: 0.6870 (tpp) cc_final: 0.6481 (mmt) REVERT: E 73 ASP cc_start: 0.7222 (m-30) cc_final: 0.6517 (t70) REVERT: E 83 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.5210 (mmm) REVERT: F 73 ASP cc_start: 0.7210 (m-30) cc_final: 0.6527 (t70) REVERT: G 73 ASP cc_start: 0.7027 (m-30) cc_final: 0.6568 (t70) REVERT: H 22 SER cc_start: 0.7512 (t) cc_final: 0.7098 (p) REVERT: H 73 ASP cc_start: 0.7131 (m-30) cc_final: 0.6372 (t70) REVERT: H 83 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5031 (mmm) REVERT: B 114 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7472 (tpp80) REVERT: B 137 MET cc_start: 0.8366 (mmp) cc_final: 0.7876 (tpt) REVERT: B 141 ASP cc_start: 0.6805 (t70) cc_final: 0.6525 (t0) REVERT: B 247 SER cc_start: 0.8777 (t) cc_final: 0.8447 (p) REVERT: C 114 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7494 (mmt180) REVERT: C 137 MET cc_start: 0.7727 (mmm) cc_final: 0.7478 (mmp) REVERT: C 141 ASP cc_start: 0.6905 (t70) cc_final: 0.6587 (t0) REVERT: C 170 ARG cc_start: 0.8745 (mtt90) cc_final: 0.8460 (mtt90) REVERT: D 114 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7495 (tpp80) REVERT: D 141 ASP cc_start: 0.6831 (t70) cc_final: 0.6540 (t0) REVERT: D 196 LYS cc_start: 0.7407 (ttpt) cc_final: 0.7095 (mtpt) outliers start: 27 outliers final: 21 residues processed: 206 average time/residue: 0.1223 time to fit residues: 37.0623 Evaluate side-chains 193 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 443 THR Chi-restraints excluded: chain D residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 44 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 167 optimal weight: 0.0370 chunk 139 optimal weight: 0.0770 chunk 116 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 137 optimal weight: 0.0980 chunk 48 optimal weight: 30.0000 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.210716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146468 restraints weight = 15243.964| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.67 r_work: 0.3110 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3024 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= 0.101 Angle : 0.481 7.574 21188 Z= 0.254 Chirality : 0.039 0.115 2332 Planarity : 0.004 0.046 2700 Dihedral : 4.294 45.036 2136 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.64 % Allowed : 17.17 % Favored : 81.19 % 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: 1.68 (0.21), residues: 1876 helix: 2.01 (0.18), residues: 900 sheet: 0.52 (0.37), residues: 220 loop : 0.30 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 170 TYR 0.012 0.001 TYR A 161 PHE 0.035 0.001 PHE C 197 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (15644) covalent geometry : angle 0.48085 / 0.25 (21180) SS BOND : bond 0.00048 / 0.03 ( 4) SS BOND : angle 0.76939 / 0.41 ( 8) hydrogen bonds : bond 0.03139 / 2.06 ( 816) hydrogen bonds : angle 3.70018 / 2.56 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.69 seconds wall clock time: 73 minutes 47.85 seconds (4427.85 seconds total)