Starting phenix.real_space_refine on Thu Feb 5 06:30:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cty_45922/02_2026/9cty_45922.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cty_45922/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cty_45922/02_2026/9cty_45922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cty_45922/02_2026/9cty_45922.map" model { file = "/net/cci-nas-00/data/ceres_data/9cty_45922/02_2026/9cty_45922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cty_45922/02_2026/9cty_45922.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15280 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "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, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.34, per 1000 atoms: 0.22 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: 1.34 Conformation dependent library (CDL) restraints added in 573.0 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: 0.53 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: 2.55 Time building geometry restraints manager: 1.83 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: 8.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.920 Find NCS groups from input model: 0.280 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 covalent geometry : bond 0.01113 (15644) covalent geometry : angle 1.11592 (21180) SS BOND : bond 0.03348 ( 4) SS BOND : angle 1.96379 ( 8) hydrogen bonds : bond 0.14427 ( 816) hydrogen bonds : angle 6.37220 ( 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 : 0.390 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: 0.1326 time to fit residues: 61.3622 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 : 0.403 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.209215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143758 restraints weight = 15109.226| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.81 r_work: 0.3078 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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= 0.139 Angle : 0.532 5.463 21188 Z= 0.281 Chirality : 0.041 0.120 2332 Planarity : 0.005 0.042 2700 Dihedral : 5.990 56.215 2175 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.49 % Allowed : 11.10 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1876 helix: 1.02 (0.18), residues: 880 sheet: 0.01 (0.37), residues: 212 loop : -0.25 (0.24), 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 covalent geometry : bond 0.00325 (15644) covalent geometry : angle 0.53183 (21180) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.92952 ( 8) hydrogen bonds : bond 0.03979 ( 816) hydrogen bonds : angle 4.60925 ( 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: 41 poor density : 211 time to evaluate : 0.606 Fit side-chains REVERT: A 114 ARG cc_start: 0.8286 (ttm170) cc_final: 0.7664 (mmt180) REVERT: A 141 ASP cc_start: 0.7213 (t70) cc_final: 0.6638 (t0) REVERT: A 194 MET cc_start: 0.6915 (tpp) cc_final: 0.6692 (mmt) REVERT: A 205 ARG cc_start: 0.5113 (OUTLIER) cc_final: 0.4661 (mtp180) REVERT: A 389 GLN cc_start: 0.9021 (mt0) cc_final: 0.8814 (mt0) REVERT: E 73 ASP cc_start: 0.7211 (m-30) cc_final: 0.6587 (t70) REVERT: F 73 ASP cc_start: 0.7145 (m-30) cc_final: 0.6534 (t70) REVERT: G 73 ASP cc_start: 0.7282 (m-30) cc_final: 0.6786 (t70) REVERT: H 22 SER cc_start: 0.7726 (t) cc_final: 0.7506 (p) REVERT: B 114 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7629 (ttm-80) REVERT: B 137 MET cc_start: 0.7791 (mmm) cc_final: 0.7542 (tpt) REVERT: B 140 PHE cc_start: 0.8158 (t80) cc_final: 0.7890 (t80) REVERT: B 141 ASP cc_start: 0.7113 (t70) cc_final: 0.6601 (t0) REVERT: B 205 ARG cc_start: 0.5404 (OUTLIER) cc_final: 0.4854 (mtp180) REVERT: B 389 GLN cc_start: 0.8993 (mt0) cc_final: 0.8790 (mt0) REVERT: C 114 ARG cc_start: 0.8224 (ttm170) cc_final: 0.7640 (mmt180) REVERT: C 137 MET cc_start: 0.7682 (mmm) cc_final: 0.7439 (tpt) REVERT: C 140 PHE cc_start: 0.8222 (t80) cc_final: 0.7934 (t80) REVERT: C 141 ASP cc_start: 0.7205 (t70) cc_final: 0.6702 (t0) REVERT: C 194 MET cc_start: 0.6986 (tpp) cc_final: 0.6644 (mmt) REVERT: C 205 ARG cc_start: 0.5097 (OUTLIER) cc_final: 0.4677 (mtp180) REVERT: C 389 GLN cc_start: 0.9020 (mt0) cc_final: 0.8815 (mt0) REVERT: D 114 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7588 (mmt180) REVERT: D 137 MET cc_start: 0.7747 (mmm) cc_final: 0.7486 (tpt) REVERT: D 140 PHE cc_start: 0.8115 (t80) cc_final: 0.7816 (t80) REVERT: D 141 ASP cc_start: 0.7120 (t70) cc_final: 0.6670 (t0) REVERT: D 205 ARG cc_start: 0.5225 (OUTLIER) cc_final: 0.4758 (mtp180) outliers start: 41 outliers final: 21 residues processed: 235 average time/residue: 0.1506 time to fit residues: 50.2250 Evaluate side-chains 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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: 3.9990 chunk 184 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 16 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4279 r_free = 0.4279 target = 0.210400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144340 restraints weight = 15186.503| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.23 r_work: 0.3149 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2070 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= 0.123 Angle : 0.491 5.524 21188 Z= 0.261 Chirality : 0.040 0.119 2332 Planarity : 0.004 0.044 2700 Dihedral : 5.525 51.936 2168 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.61 % Allowed : 12.74 % Favored : 84.65 % 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: 1.03 (0.21), residues: 1876 helix: 1.39 (0.18), residues: 888 sheet: 0.23 (0.37), residues: 212 loop : 0.12 (0.25), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.012 0.001 TYR G 94 PHE 0.012 0.001 PHE C 197 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00290 (15644) covalent geometry : angle 0.49123 (21180) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.88267 ( 8) hydrogen bonds : bond 0.03694 ( 816) hydrogen bonds : angle 4.28722 ( 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 236 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.406 Fit side-chains REVERT: A 114 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7585 (mmt180) REVERT: A 137 MET cc_start: 0.7894 (tpt) cc_final: 0.7580 (mmm) REVERT: A 141 ASP cc_start: 0.7169 (t70) cc_final: 0.6633 (t0) REVERT: A 205 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.4637 (mtp180) REVERT: E 73 ASP cc_start: 0.7255 (m-30) cc_final: 0.6543 (t70) REVERT: E 83 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.5378 (mmm) REVERT: F 57 SER cc_start: 0.6706 (t) cc_final: 0.6499 (m) REVERT: F 73 ASP cc_start: 0.7155 (m-30) cc_final: 0.6473 (t70) REVERT: G 73 ASP cc_start: 0.7249 (m-30) cc_final: 0.6662 (t70) REVERT: H 22 SER cc_start: 0.7716 (t) cc_final: 0.7428 (p) REVERT: H 83 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.5341 (mmm) REVERT: B 114 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7604 (ttm170) REVERT: B 137 MET cc_start: 0.7835 (mmm) cc_final: 0.7594 (tpt) REVERT: B 141 ASP cc_start: 0.7178 (t70) cc_final: 0.6650 (t0) REVERT: B 205 ARG cc_start: 0.5256 (OUTLIER) cc_final: 0.4732 (mtp180) REVERT: B 247 SER cc_start: 0.8835 (t) cc_final: 0.8488 (p) REVERT: B 365 VAL cc_start: 0.8102 (p) cc_final: 0.7763 (m) REVERT: C 114 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7660 (ttm-80) REVERT: C 137 MET cc_start: 0.7639 (mmm) cc_final: 0.7398 (mmp) REVERT: C 141 ASP cc_start: 0.7205 (t70) cc_final: 0.6667 (t0) REVERT: C 205 ARG cc_start: 0.5071 (OUTLIER) cc_final: 0.4650 (mtp180) REVERT: D 114 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7602 (mmt180) REVERT: D 141 ASP cc_start: 0.7130 (t70) cc_final: 0.6622 (t0) REVERT: D 205 ARG cc_start: 0.5177 (OUTLIER) cc_final: 0.4708 (mtp180) outliers start: 43 outliers final: 18 residues processed: 223 average time/residue: 0.1243 time to fit residues: 40.4623 Evaluate side-chains 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 102 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.205812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144281 restraints weight = 15191.614| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.77 r_work: 0.3012 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2367 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= 0.205 Angle : 0.548 5.698 21188 Z= 0.291 Chirality : 0.043 0.126 2332 Planarity : 0.005 0.049 2700 Dihedral : 5.277 52.418 2152 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.55 % Allowed : 13.90 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1876 helix: 1.28 (0.18), residues: 884 sheet: 0.34 (0.37), residues: 212 loop : 0.24 (0.25), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 396 TYR 0.013 0.001 TYR E 106 PHE 0.019 0.001 PHE D 197 TRP 0.009 0.002 TRP A 436 HIS 0.002 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00505 (15644) covalent geometry : angle 0.54749 (21180) SS BOND : bond 0.00257 ( 4) SS BOND : angle 1.47134 ( 8) hydrogen bonds : bond 0.04221 ( 816) hydrogen bonds : angle 4.33953 ( 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 221 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.608 Fit side-chains REVERT: A 114 ARG cc_start: 0.8293 (ttm170) cc_final: 0.7702 (mmt180) REVERT: A 137 MET cc_start: 0.7931 (tpt) cc_final: 0.7682 (mmm) REVERT: A 141 ASP cc_start: 0.7305 (t70) cc_final: 0.6886 (t0) REVERT: A 205 ARG cc_start: 0.5208 (OUTLIER) cc_final: 0.4691 (mtp180) REVERT: E 73 ASP cc_start: 0.7362 (m-30) cc_final: 0.6782 (t70) REVERT: E 83 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.5534 (mmm) REVERT: F 73 ASP cc_start: 0.7341 (m-30) cc_final: 0.6793 (t70) REVERT: G 73 ASP cc_start: 0.7365 (m-30) cc_final: 0.6839 (t70) REVERT: H 22 SER cc_start: 0.7927 (t) cc_final: 0.7640 (p) REVERT: H 73 ASP cc_start: 0.7351 (m-30) cc_final: 0.6703 (t70) REVERT: H 83 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.5494 (mmm) REVERT: B 114 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7678 (tpp80) REVERT: B 141 ASP cc_start: 0.7273 (t70) cc_final: 0.6782 (t0) REVERT: B 205 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.4852 (mtp180) REVERT: B 247 SER cc_start: 0.8875 (t) cc_final: 0.8542 (p) REVERT: C 114 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7673 (tpp80) REVERT: C 137 MET cc_start: 0.7709 (mmm) cc_final: 0.7464 (mmp) REVERT: C 141 ASP cc_start: 0.7311 (t70) cc_final: 0.6874 (t0) REVERT: C 205 ARG cc_start: 0.5197 (OUTLIER) cc_final: 0.4683 (mtp180) REVERT: C 395 MET cc_start: 0.8282 (mmt) cc_final: 0.7985 (mmt) REVERT: D 114 ARG cc_start: 0.8313 (ttm170) cc_final: 0.7753 (ttm-80) REVERT: D 141 ASP cc_start: 0.7249 (t70) cc_final: 0.6744 (t0) REVERT: D 205 ARG cc_start: 0.5319 (OUTLIER) cc_final: 0.4749 (mtp180) outliers start: 42 outliers final: 22 residues processed: 201 average time/residue: 0.1419 time to fit residues: 41.0604 Evaluate side-chains 193 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 78 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 194 MET 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: 0.5980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 163 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN B 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.208598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140200 restraints weight = 15207.079| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.06 r_work: 0.3059 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2485 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= 0.113 Angle : 0.479 5.541 21188 Z= 0.253 Chirality : 0.040 0.124 2332 Planarity : 0.004 0.046 2700 Dihedral : 5.040 52.729 2152 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.06 % Allowed : 14.68 % Favored : 83.25 % 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: 1.51 (0.18), residues: 892 sheet: 0.67 (0.37), residues: 212 loop : 0.28 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 135 TYR 0.009 0.001 TYR A 161 PHE 0.021 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 covalent geometry : bond 0.00261 (15644) covalent geometry : angle 0.47840 (21180) SS BOND : bond 0.00032 ( 4) SS BOND : angle 0.87782 ( 8) hydrogen bonds : bond 0.03452 ( 816) hydrogen bonds : angle 4.00618 ( 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 211 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7608 (mpt180) REVERT: A 137 MET cc_start: 0.7807 (tpt) cc_final: 0.7587 (mmm) REVERT: A 141 ASP cc_start: 0.7133 (t70) cc_final: 0.6744 (t0) REVERT: A 205 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.4600 (mtp180) REVERT: E 73 ASP cc_start: 0.7211 (m-30) cc_final: 0.6610 (t70) REVERT: E 83 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.5386 (mmm) REVERT: F 73 ASP cc_start: 0.7232 (m-30) cc_final: 0.6634 (t70) REVERT: G 73 ASP cc_start: 0.7291 (m-30) cc_final: 0.6733 (t70) REVERT: H 22 SER cc_start: 0.7638 (t) cc_final: 0.7284 (p) REVERT: H 83 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.5130 (mmm) REVERT: B 114 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7508 (tpp80) REVERT: B 137 MET cc_start: 0.8098 (tpt) cc_final: 0.7880 (mmm) REVERT: B 141 ASP cc_start: 0.7081 (t70) cc_final: 0.6692 (t0) REVERT: B 205 ARG cc_start: 0.5151 (OUTLIER) cc_final: 0.4706 (mtp180) REVERT: B 247 SER cc_start: 0.8707 (t) cc_final: 0.8432 (p) REVERT: C 114 ARG cc_start: 0.8086 (ttm170) cc_final: 0.7578 (mpt180) REVERT: C 137 MET cc_start: 0.7551 (mmm) cc_final: 0.7307 (mmp) REVERT: C 141 ASP cc_start: 0.7216 (t70) cc_final: 0.6791 (t0) REVERT: C 194 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6607 (mmt) REVERT: C 205 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.4585 (mtp180) REVERT: D 114 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7570 (mpt180) REVERT: D 141 ASP cc_start: 0.7123 (t70) cc_final: 0.6656 (t0) REVERT: D 205 ARG cc_start: 0.5172 (OUTLIER) cc_final: 0.4689 (mtp180) outliers start: 34 outliers final: 13 residues processed: 202 average time/residue: 0.1425 time to fit residues: 41.8276 Evaluate side-chains 179 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 E residue 83 MET 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 166 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.206933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137424 restraints weight = 15150.123| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.93 r_work: 0.3091 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15648 Z= 0.149 Angle : 0.505 5.712 21188 Z= 0.268 Chirality : 0.041 0.122 2332 Planarity : 0.004 0.047 2700 Dihedral : 5.088 52.993 2152 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 14.81 % Favored : 83.19 % 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: 1.35 (0.21), residues: 1876 helix: 1.55 (0.18), residues: 892 sheet: 0.76 (0.38), residues: 212 loop : 0.28 (0.25), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100 TYR 0.008 0.001 TYR G 106 PHE 0.017 0.001 PHE C 140 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00362 (15644) covalent geometry : angle 0.50471 (21180) SS BOND : bond 0.00146 ( 4) SS BOND : angle 1.19250 ( 8) hydrogen bonds : bond 0.03770 ( 816) hydrogen bonds : angle 3.96897 ( 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 210 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.568 Fit side-chains REVERT: A 114 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7574 (mpt180) REVERT: A 137 MET cc_start: 0.7820 (tpt) cc_final: 0.7594 (mmm) REVERT: A 141 ASP cc_start: 0.7111 (t70) cc_final: 0.6740 (t0) REVERT: A 205 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.4631 (mtp180) REVERT: A 395 MET cc_start: 0.8233 (mmt) cc_final: 0.7988 (mmt) REVERT: E 73 ASP cc_start: 0.7221 (m-30) cc_final: 0.6647 (t70) REVERT: E 83 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.5425 (mmm) REVERT: F 73 ASP cc_start: 0.7206 (m-30) cc_final: 0.6625 (t70) REVERT: G 73 ASP cc_start: 0.7130 (m-30) cc_final: 0.6764 (t70) REVERT: H 22 SER cc_start: 0.7681 (t) cc_final: 0.7360 (p) REVERT: H 73 ASP cc_start: 0.7206 (m-30) cc_final: 0.6525 (t70) REVERT: H 83 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.5197 (mmm) REVERT: B 114 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7446 (tpp80) REVERT: B 137 MET cc_start: 0.8116 (tpt) cc_final: 0.7829 (mmm) REVERT: B 141 ASP cc_start: 0.7124 (t70) cc_final: 0.6712 (t0) REVERT: B 205 ARG cc_start: 0.5114 (OUTLIER) cc_final: 0.4660 (mtp180) REVERT: B 247 SER cc_start: 0.8744 (t) cc_final: 0.8429 (p) REVERT: B 365 VAL cc_start: 0.8101 (p) cc_final: 0.7816 (m) REVERT: C 114 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7480 (tpp80) REVERT: C 137 MET cc_start: 0.7610 (mmm) cc_final: 0.7377 (mmp) REVERT: C 141 ASP cc_start: 0.7188 (t70) cc_final: 0.6780 (t0) REVERT: C 205 ARG cc_start: 0.5044 (OUTLIER) cc_final: 0.4612 (mtp180) REVERT: D 114 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7484 (tpp80) REVERT: D 137 MET cc_start: 0.8259 (mmp) cc_final: 0.7804 (tpt) REVERT: D 141 ASP cc_start: 0.7135 (t70) cc_final: 0.6756 (t0) REVERT: D 205 ARG cc_start: 0.5090 (OUTLIER) cc_final: 0.4617 (mtp180) REVERT: D 395 MET cc_start: 0.8245 (mmt) cc_final: 0.8008 (mmt) outliers start: 33 outliers final: 17 residues processed: 199 average time/residue: 0.1437 time to fit residues: 41.3668 Evaluate side-chains 186 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 106 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.2980 chunk 142 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.208695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140353 restraints weight = 15016.601| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.15 r_work: 0.3054 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15648 Z= 0.109 Angle : 0.479 6.362 21188 Z= 0.251 Chirality : 0.040 0.116 2332 Planarity : 0.004 0.045 2700 Dihedral : 4.959 53.051 2152 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.40 % Allowed : 15.96 % Favored : 82.65 % 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: 1.49 (0.21), residues: 1876 helix: 1.74 (0.18), residues: 892 sheet: 0.55 (0.37), residues: 220 loop : 0.34 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100 TYR 0.009 0.001 TYR H 104 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 covalent geometry : bond 0.00254 (15644) covalent geometry : angle 0.47835 (21180) SS BOND : bond 0.00046 ( 4) SS BOND : angle 0.93273 ( 8) hydrogen bonds : bond 0.03407 ( 816) hydrogen bonds : angle 3.87218 ( 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 194 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.644 Fit side-chains REVERT: A 114 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7599 (mpt180) REVERT: A 137 MET cc_start: 0.7803 (tpt) cc_final: 0.7545 (mmm) REVERT: A 141 ASP cc_start: 0.7065 (t70) cc_final: 0.6733 (t0) REVERT: A 205 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.4609 (mtp180) REVERT: E 73 ASP cc_start: 0.7238 (m-30) cc_final: 0.6661 (t70) REVERT: E 83 MET cc_start: 0.6653 (OUTLIER) cc_final: 0.5472 (mmm) REVERT: F 73 ASP cc_start: 0.7222 (m-30) cc_final: 0.6637 (t70) REVERT: G 73 ASP cc_start: 0.7164 (m-30) cc_final: 0.6783 (t70) REVERT: H 22 SER cc_start: 0.7635 (t) cc_final: 0.7229 (p) REVERT: H 73 ASP cc_start: 0.7200 (m-30) cc_final: 0.6515 (t70) REVERT: H 83 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5197 (mmm) REVERT: B 114 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7474 (tpp80) REVERT: B 137 MET cc_start: 0.8080 (tpt) cc_final: 0.7765 (mmm) REVERT: B 141 ASP cc_start: 0.7038 (t70) cc_final: 0.6700 (t0) REVERT: B 205 ARG cc_start: 0.5062 (OUTLIER) cc_final: 0.4631 (mtp180) REVERT: B 247 SER cc_start: 0.8711 (t) cc_final: 0.8439 (p) REVERT: B 365 VAL cc_start: 0.8146 (p) cc_final: 0.7852 (m) REVERT: C 114 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7584 (mpt180) REVERT: C 137 MET cc_start: 0.7654 (mmm) cc_final: 0.7415 (mmp) REVERT: C 141 ASP cc_start: 0.7027 (t70) cc_final: 0.6696 (t0) REVERT: C 205 ARG cc_start: 0.5027 (OUTLIER) cc_final: 0.4619 (mtp180) REVERT: C 395 MET cc_start: 0.8189 (mmt) cc_final: 0.7950 (mmt) REVERT: D 114 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7572 (mpt180) REVERT: D 137 MET cc_start: 0.8290 (mmp) cc_final: 0.7823 (tpt) REVERT: D 141 ASP cc_start: 0.7032 (t70) cc_final: 0.6671 (t0) REVERT: D 205 ARG cc_start: 0.5064 (OUTLIER) cc_final: 0.4614 (mtp180) REVERT: D 365 VAL cc_start: 0.8088 (p) cc_final: 0.7807 (m) outliers start: 23 outliers final: 14 residues processed: 188 average time/residue: 0.1503 time to fit residues: 40.5006 Evaluate side-chains 184 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 E residue 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER 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 258 GLU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 160 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.206355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141476 restraints weight = 15263.376| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.38 r_work: 0.3027 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15648 Z= 0.176 Angle : 0.522 5.872 21188 Z= 0.276 Chirality : 0.042 0.126 2332 Planarity : 0.004 0.047 2700 Dihedral : 5.115 53.381 2152 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.64 % Allowed : 15.96 % 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: 1.34 (0.21), residues: 1876 helix: 1.59 (0.18), residues: 896 sheet: 0.56 (0.37), residues: 220 loop : 0.26 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 100 TYR 0.017 0.001 TYR H 104 PHE 0.018 0.001 PHE C 197 TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00434 (15644) covalent geometry : angle 0.52106 (21180) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.30089 ( 8) hydrogen bonds : bond 0.03885 ( 816) hydrogen bonds : angle 3.95814 ( 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 205 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.429 Fit side-chains REVERT: A 114 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7642 (mpt180) REVERT: A 137 MET cc_start: 0.7808 (tpt) cc_final: 0.7538 (mmm) REVERT: A 141 ASP cc_start: 0.6992 (t70) cc_final: 0.6637 (t0) REVERT: A 365 VAL cc_start: 0.8060 (p) cc_final: 0.7771 (m) REVERT: E 73 ASP cc_start: 0.7222 (m-30) cc_final: 0.6587 (t70) REVERT: E 83 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5325 (mmm) REVERT: F 73 ASP cc_start: 0.7188 (m-30) cc_final: 0.6537 (t70) REVERT: G 73 ASP cc_start: 0.7062 (m-30) cc_final: 0.6623 (t70) REVERT: H 22 SER cc_start: 0.7703 (t) cc_final: 0.7363 (p) REVERT: H 73 ASP cc_start: 0.7194 (m-30) cc_final: 0.6467 (t70) REVERT: H 83 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.4993 (mmm) REVERT: B 114 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7511 (tpp80) REVERT: B 137 MET cc_start: 0.8090 (tpt) cc_final: 0.7741 (mmm) REVERT: B 141 ASP cc_start: 0.6993 (t70) cc_final: 0.6629 (t0) REVERT: B 205 ARG cc_start: 0.5077 (OUTLIER) cc_final: 0.4623 (mtp180) REVERT: B 247 SER cc_start: 0.8845 (t) cc_final: 0.8497 (p) REVERT: C 114 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7537 (tpp80) REVERT: C 137 MET cc_start: 0.7719 (mmm) cc_final: 0.7480 (mmp) REVERT: C 141 ASP cc_start: 0.7014 (t70) cc_final: 0.6651 (t0) REVERT: C 395 MET cc_start: 0.8319 (mmt) cc_final: 0.8060 (mmt) REVERT: D 114 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7541 (tpp80) REVERT: D 137 MET cc_start: 0.8345 (mmp) cc_final: 0.7825 (tpt) REVERT: D 141 ASP cc_start: 0.6901 (t70) cc_final: 0.6556 (t0) outliers start: 27 outliers final: 14 residues processed: 197 average time/residue: 0.1339 time to fit residues: 38.3805 Evaluate side-chains 186 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 H residue 83 MET 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 258 GLU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 4 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.204878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135734 restraints weight = 15189.013| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.90 r_work: 0.2988 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15648 Z= 0.226 Angle : 0.562 5.776 21188 Z= 0.298 Chirality : 0.043 0.131 2332 Planarity : 0.005 0.048 2700 Dihedral : 4.960 53.338 2140 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.33 % Allowed : 16.50 % Favored : 82.16 % 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: 1.12 (0.21), residues: 1876 helix: 1.37 (0.17), residues: 892 sheet: 0.46 (0.37), residues: 220 loop : 0.23 (0.25), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 32 TYR 0.027 0.002 TYR H 104 PHE 0.019 0.002 PHE D 140 TRP 0.009 0.002 TRP A 436 HIS 0.001 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00560 (15644) covalent geometry : angle 0.56143 (21180) SS BOND : bond 0.00295 ( 4) SS BOND : angle 1.59646 ( 8) hydrogen bonds : bond 0.04248 ( 816) hydrogen bonds : angle 4.08561 ( 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 203 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.589 Fit side-chains REVERT: A 114 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7508 (mpt180) REVERT: A 137 MET cc_start: 0.7807 (tpt) cc_final: 0.7595 (mmm) REVERT: A 141 ASP cc_start: 0.7022 (t70) cc_final: 0.6653 (t0) REVERT: E 73 ASP cc_start: 0.7206 (m-30) cc_final: 0.6604 (t70) REVERT: E 83 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5359 (mmm) REVERT: F 73 ASP cc_start: 0.7173 (m-30) cc_final: 0.6584 (t70) REVERT: G 73 ASP cc_start: 0.7057 (m-30) cc_final: 0.6651 (t70) REVERT: H 22 SER cc_start: 0.7848 (t) cc_final: 0.7484 (p) REVERT: H 73 ASP cc_start: 0.7161 (m-30) cc_final: 0.6486 (t70) REVERT: H 83 MET cc_start: 0.5891 (OUTLIER) cc_final: 0.4967 (mmm) REVERT: B 114 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7436 (ttm-80) REVERT: B 137 MET cc_start: 0.8035 (tpt) cc_final: 0.7734 (mmm) REVERT: B 141 ASP cc_start: 0.7041 (t70) cc_final: 0.6633 (t0) REVERT: B 205 ARG cc_start: 0.5197 (OUTLIER) cc_final: 0.4921 (ptm160) REVERT: B 247 SER cc_start: 0.8759 (t) cc_final: 0.8365 (p) REVERT: B 395 MET cc_start: 0.8112 (mmt) cc_final: 0.7843 (mmp) REVERT: C 114 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7427 (tpp80) REVERT: C 137 MET cc_start: 0.7674 (mmm) cc_final: 0.7431 (mmp) REVERT: C 141 ASP cc_start: 0.6984 (t70) cc_final: 0.6606 (t0) REVERT: C 395 MET cc_start: 0.8109 (mmt) cc_final: 0.7810 (mmt) REVERT: D 114 ARG cc_start: 0.8060 (ttm170) cc_final: 0.7426 (tpp80) REVERT: D 141 ASP cc_start: 0.6976 (t70) cc_final: 0.6585 (t0) outliers start: 22 outliers final: 13 residues processed: 194 average time/residue: 0.1303 time to fit residues: 36.4393 Evaluate side-chains 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 MET Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 57 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 260 ARG Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 171 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 112 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.207669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139354 restraints weight = 15182.800| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.69 r_work: 0.3084 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15648 Z= 0.117 Angle : 0.491 7.660 21188 Z= 0.260 Chirality : 0.040 0.117 2332 Planarity : 0.004 0.047 2700 Dihedral : 4.653 53.256 2140 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.85 % Allowed : 17.11 % Favored : 82.04 % 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: 1.35 (0.21), residues: 1876 helix: 1.64 (0.18), residues: 900 sheet: 0.47 (0.37), residues: 220 loop : 0.25 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 396 TYR 0.017 0.001 TYR H 104 PHE 0.018 0.001 PHE A 140 TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 380 Details of bonding type rmsd covalent geometry : bond 0.00277 (15644) covalent geometry : angle 0.49099 (21180) SS BOND : bond 0.00034 ( 4) SS BOND : angle 0.90649 ( 8) hydrogen bonds : bond 0.03451 ( 816) hydrogen bonds : angle 3.89713 ( 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 198 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 114 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7499 (mpt180) REVERT: A 137 MET cc_start: 0.7806 (tpt) cc_final: 0.7563 (mmm) REVERT: A 141 ASP cc_start: 0.6960 (t70) cc_final: 0.6627 (t0) REVERT: E 73 ASP cc_start: 0.7197 (m-30) cc_final: 0.6549 (t70) REVERT: E 83 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5239 (mmm) REVERT: F 73 ASP cc_start: 0.7161 (m-30) cc_final: 0.6562 (t70) REVERT: G 73 ASP cc_start: 0.6935 (m-30) cc_final: 0.6628 (t70) REVERT: H 22 SER cc_start: 0.7582 (t) cc_final: 0.7198 (p) REVERT: H 73 ASP cc_start: 0.7177 (m-30) cc_final: 0.6506 (t70) REVERT: H 83 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.4992 (mmm) REVERT: B 114 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7428 (tpp80) REVERT: B 137 MET cc_start: 0.8082 (tpt) cc_final: 0.7763 (mmm) REVERT: B 141 ASP cc_start: 0.6947 (t70) cc_final: 0.6614 (t0) REVERT: B 205 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.4709 (mtp180) REVERT: B 247 SER cc_start: 0.8684 (t) cc_final: 0.8409 (p) REVERT: C 137 MET cc_start: 0.7645 (mmm) cc_final: 0.7414 (mmp) REVERT: C 141 ASP cc_start: 0.7011 (t70) cc_final: 0.6678 (t0) REVERT: C 395 MET cc_start: 0.8131 (mmt) cc_final: 0.7869 (mmt) REVERT: D 114 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7466 (mpt180) REVERT: D 137 MET cc_start: 0.8391 (mmp) cc_final: 0.8099 (mmm) REVERT: D 141 ASP cc_start: 0.6924 (t70) cc_final: 0.6590 (t0) outliers start: 14 outliers final: 10 residues processed: 190 average time/residue: 0.1315 time to fit residues: 36.3429 Evaluate side-chains 197 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 MET Chi-restraints excluded: chain F 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 260 ARG Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 44 optimal weight: 8.9990 chunk 152 optimal weight: 0.0980 chunk 167 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 137 optimal weight: 0.0020 chunk 48 optimal weight: 30.0000 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.209392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140476 restraints weight = 15142.961| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.70 r_work: 0.3160 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15648 Z= 0.103 Angle : 0.475 7.393 21188 Z= 0.251 Chirality : 0.039 0.114 2332 Planarity : 0.004 0.047 2700 Dihedral : 4.490 53.182 2140 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.91 % Allowed : 17.11 % Favored : 81.98 % 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: 1.59 (0.21), residues: 1876 helix: 1.92 (0.18), residues: 900 sheet: 0.53 (0.37), residues: 220 loop : 0.26 (0.26), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 100 TYR 0.016 0.001 TYR H 104 PHE 0.017 0.001 PHE B 140 TRP 0.009 0.001 TRP A 436 HIS 0.001 0.000 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00234 (15644) covalent geometry : angle 0.47522 (21180) SS BOND : bond 0.00045 ( 4) SS BOND : angle 0.78956 ( 8) hydrogen bonds : bond 0.03224 ( 816) hydrogen bonds : angle 3.77788 ( 2448) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4426.41 seconds wall clock time: 76 minutes 18.41 seconds (4578.41 seconds total)