Starting phenix.real_space_refine on Wed Mar 4 05:55:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkf_23871/03_2026/7mkf_23871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkf_23871/03_2026/7mkf_23871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mkf_23871/03_2026/7mkf_23871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkf_23871/03_2026/7mkf_23871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mkf_23871/03_2026/7mkf_23871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkf_23871/03_2026/7mkf_23871.map" } resolution = 3.0 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= 0.004 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 S 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 H 5800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.79, per 1000 atoms: 0.16 Number of scatterers: 11370 At special positions: 0 Unit cell: (97.02, 137.984, 45.276, 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) S 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 6.00 H 5800 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 368.9 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 326 removed outlier: 6.346A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY E 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N CYS C 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU E 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N SER C 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LYS G 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER E 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY G 323 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N CYS E 322 " --> pdb=" O GLY G 323 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU G 325 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER E 324 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL G 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS I 321 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER G 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY I 323 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N CYS G 322 " --> pdb=" O GLY I 323 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU I 325 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER G 324 " --> pdb=" O LEU I 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.582A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL E 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS G 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL E 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL G 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LYS I 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL G 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.440A pdb=" N LEU A 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS C 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE A 346 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS E 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE C 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU E 344 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LYS G 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE E 346 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU G 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS I 347 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE G 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.832A pdb=" N SER A 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER C 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER E 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER G 356 " --> pdb=" O GLY I 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.369A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR E 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR G 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 367 through 377 Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 324 removed outlier: 6.409A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLY D 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LYS F 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLY F 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N CYS D 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL F 318 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS H 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER F 320 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLY H 323 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N CYS F 322 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL H 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS J 321 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER H 320 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLY J 323 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N CYS H 322 " --> pdb=" O GLY J 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.395A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE F 328 " --> pdb=" O HIS H 329 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE H 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.538A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LYS H 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL F 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL H 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LYS J 340 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL H 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.583A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE F 346 " --> pdb=" O LYS H 347 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE H 346 " --> pdb=" O LYS J 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 350 through 356 removed outlier: 6.889A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER D 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER F 356 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER H 356 " --> pdb=" O GLY J 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.345A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR H 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 367 through 377 152 hydrogen bonds defined for protein. 456 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: 2.04 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 5790 1.12 - 1.29: 930 1.29 - 1.45: 1813 1.45 - 1.62: 2917 1.62 - 1.78: 10 Bond restraints: 11460 Sorted by residual: bond pdb=" NE2 HIS D 374 " pdb=" HE2 HIS D 374 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" NE2 HIS B 374 " pdb=" HE2 HIS B 374 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" NE2 HIS J 374 " pdb=" HE2 HIS J 374 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.51e+01 bond pdb=" NE2 HIS F 374 " pdb=" HE2 HIS F 374 " ideal model delta sigma weight residual 0.860 1.055 -0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" NE2 HIS H 374 " pdb=" HE2 HIS H 374 " ideal model delta sigma weight residual 0.860 1.054 -0.194 2.00e-02 2.50e+03 9.44e+01 ... (remaining 11455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 18252 3.12 - 6.24: 1904 6.24 - 9.36: 674 9.36 - 12.49: 70 12.49 - 15.61: 10 Bond angle restraints: 20910 Sorted by residual: angle pdb=" N SER H 352 " pdb=" CA SER H 352 " pdb=" C SER H 352 " ideal model delta sigma weight residual 108.99 117.43 -8.44 1.57e+00 4.06e-01 2.89e+01 angle pdb=" N SER J 352 " pdb=" CA SER J 352 " pdb=" C SER J 352 " ideal model delta sigma weight residual 108.99 117.42 -8.43 1.57e+00 4.06e-01 2.89e+01 angle pdb=" N SER D 352 " pdb=" CA SER D 352 " pdb=" C SER D 352 " ideal model delta sigma weight residual 108.99 117.41 -8.42 1.57e+00 4.06e-01 2.88e+01 angle pdb=" N SER F 352 " pdb=" CA SER F 352 " pdb=" C SER F 352 " ideal model delta sigma weight residual 108.99 117.40 -8.41 1.57e+00 4.06e-01 2.87e+01 angle pdb=" N SER B 352 " pdb=" CA SER B 352 " pdb=" C SER B 352 " ideal model delta sigma weight residual 108.99 117.38 -8.39 1.57e+00 4.06e-01 2.86e+01 ... (remaining 20905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 4895 15.41 - 30.83: 185 30.83 - 46.24: 100 46.24 - 61.66: 75 61.66 - 77.07: 25 Dihedral angle restraints: 5280 sinusoidal: 3010 harmonic: 2270 Sorted by residual: dihedral pdb=" CD2 HIS C 330 " pdb=" CG HIS C 330 " pdb=" ND1 HIS C 330 " pdb=" HD1 HIS C 330 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CD2 HIS E 330 " pdb=" CG HIS E 330 " pdb=" ND1 HIS E 330 " pdb=" HD1 HIS E 330 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CD2 HIS A 330 " pdb=" CG HIS A 330 " pdb=" ND1 HIS A 330 " pdb=" HD1 HIS A 330 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 342 0.051 - 0.103: 277 0.103 - 0.154: 156 0.154 - 0.206: 65 0.206 - 0.257: 20 Chirality restraints: 860 Sorted by residual: chirality pdb=" CG LEU E 357 " pdb=" CB LEU E 357 " pdb=" CD1 LEU E 357 " pdb=" CD2 LEU E 357 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CG LEU C 357 " pdb=" CB LEU C 357 " pdb=" CD1 LEU C 357 " pdb=" CD2 LEU C 357 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CG LEU G 357 " pdb=" CB LEU G 357 " pdb=" CD1 LEU G 357 " pdb=" CD2 LEU G 357 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 857 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 330 " 0.049 2.00e-02 2.50e+03 5.91e-02 7.87e+01 pdb=" CG HIS C 330 " 0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS C 330 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 HIS C 330 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS C 330 " 0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS C 330 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 HIS C 330 " -0.136 2.00e-02 2.50e+03 pdb=" HD2 HIS C 330 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 HIS C 330 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 330 " 0.049 2.00e-02 2.50e+03 5.91e-02 7.87e+01 pdb=" CG HIS A 330 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS A 330 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 HIS A 330 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS A 330 " 0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS A 330 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 HIS A 330 " -0.136 2.00e-02 2.50e+03 pdb=" HD2 HIS A 330 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 HIS A 330 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 330 " 0.049 2.00e-02 2.50e+03 5.91e-02 7.86e+01 pdb=" CG HIS E 330 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS E 330 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 HIS E 330 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS E 330 " 0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS E 330 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 HIS E 330 " -0.136 2.00e-02 2.50e+03 pdb=" HD2 HIS E 330 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 HIS E 330 " 0.038 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1381 2.21 - 2.81: 22812 2.81 - 3.41: 30411 3.41 - 4.00: 41953 4.00 - 4.60: 60840 Nonbonded interactions: 157397 Sorted by model distance: nonbonded pdb=" HZ1 LYS E 353 " pdb=" OD2 ASP E 358 " model vdw 1.615 2.450 nonbonded pdb=" HZ1 LYS A 353 " pdb=" OD2 ASP A 358 " model vdw 1.615 2.450 nonbonded pdb=" HZ1 LYS I 353 " pdb=" OD2 ASP I 358 " model vdw 1.616 2.450 nonbonded pdb=" HZ1 LYS G 353 " pdb=" OD2 ASP G 358 " model vdw 1.616 2.450 nonbonded pdb=" HZ1 LYS C 353 " pdb=" OD2 ASP C 358 " model vdw 1.616 2.450 ... (remaining 157392 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.780 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: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 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 : 0.022 0.203 5660 Z= 1.203 Angle : 1.994 9.222 7580 Z= 1.286 Chirality : 0.093 0.257 860 Planarity : 0.009 0.030 960 Dihedral : 11.334 77.072 2160 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.78 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.017 0.006 TYR F 310 PHE 0.025 0.006 PHE D 346 HIS 0.007 0.003 HIS J 374 Details of bonding type rmsd covalent geometry : bond 0.02234 ( 5660) covalent geometry : angle 1.99413 ( 7580) hydrogen bonds : bond 0.10242 ( 152) hydrogen bonds : angle 10.32971 ( 456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 282 average time/residue: 0.9754 time to fit residues: 288.8705 Evaluate side-chains 128 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 348 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 362 HIS C 362 HIS E 362 HIS G 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.111969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.100661 restraints weight = 63195.988| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 6.14 r_work: 0.4332 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 5660 Z= 0.235 Angle : 0.748 5.799 7580 Z= 0.389 Chirality : 0.051 0.175 860 Planarity : 0.004 0.037 960 Dihedral : 5.894 18.730 742 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.94 % Allowed : 21.88 % Favored : 72.19 % 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: -2.14 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 349 TYR 0.011 0.002 TYR D 310 PHE 0.015 0.002 PHE F 346 HIS 0.005 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 5660) covalent geometry : angle 0.74753 ( 7580) hydrogen bonds : bond 0.05520 ( 152) hydrogen bonds : angle 6.93255 ( 456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LEU cc_start: 0.9101 (mm) cc_final: 0.8767 (mt) REVERT: B 339 VAL cc_start: 0.9300 (t) cc_final: 0.9027 (m) REVERT: C 327 ASN cc_start: 0.9195 (m-40) cc_final: 0.8898 (p0) REVERT: C 350 VAL cc_start: 0.9290 (t) cc_final: 0.8907 (t) REVERT: C 357 LEU cc_start: 0.9205 (mp) cc_final: 0.8991 (mm) REVERT: C 371 ILE cc_start: 0.9558 (mm) cc_final: 0.9088 (mm) REVERT: C 372 GLU cc_start: 0.8830 (tp30) cc_final: 0.8184 (mp0) REVERT: E 327 ASN cc_start: 0.9263 (m-40) cc_final: 0.8805 (m-40) REVERT: E 351 GLN cc_start: 0.7994 (mt0) cc_final: 0.7679 (mp10) REVERT: F 338 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7793 (tm-30) REVERT: G 327 ASN cc_start: 0.9226 (m-40) cc_final: 0.8845 (p0) REVERT: G 344 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8940 (mp) REVERT: G 350 VAL cc_start: 0.9229 (t) cc_final: 0.8873 (t) REVERT: H 338 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7917 (tm-30) REVERT: I 327 ASN cc_start: 0.8946 (m-40) cc_final: 0.8585 (p0) REVERT: I 345 ASP cc_start: 0.8796 (m-30) cc_final: 0.8474 (p0) REVERT: J 307 GLN cc_start: 0.4824 (OUTLIER) cc_final: 0.4568 (mm-40) REVERT: J 351 GLN cc_start: 0.8080 (tt0) cc_final: 0.7845 (tp-100) outliers start: 38 outliers final: 16 residues processed: 192 average time/residue: 0.4746 time to fit residues: 100.9188 Evaluate side-chains 161 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 307 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.113653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.101927 restraints weight = 63486.338| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 6.16 r_work: 0.4385 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.7904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5660 Z= 0.200 Angle : 0.665 5.612 7580 Z= 0.343 Chirality : 0.049 0.153 860 Planarity : 0.003 0.019 960 Dihedral : 5.784 18.237 740 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.69 % Allowed : 24.69 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 349 TYR 0.012 0.002 TYR E 310 PHE 0.013 0.001 PHE F 346 HIS 0.009 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 5660) covalent geometry : angle 0.66518 ( 7580) hydrogen bonds : bond 0.04109 ( 152) hydrogen bonds : angle 6.13115 ( 456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 327 ASN cc_start: 0.9267 (m-40) cc_final: 0.8943 (p0) REVERT: C 350 VAL cc_start: 0.9281 (t) cc_final: 0.8857 (t) REVERT: C 357 LEU cc_start: 0.9337 (mp) cc_final: 0.9134 (mm) REVERT: C 371 ILE cc_start: 0.9515 (mm) cc_final: 0.9205 (mm) REVERT: D 357 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8777 (tm) REVERT: E 327 ASN cc_start: 0.9142 (m-40) cc_final: 0.8678 (p0) REVERT: E 351 GLN cc_start: 0.7818 (mt0) cc_final: 0.7557 (mp10) REVERT: E 370 LYS cc_start: 0.8848 (tttm) cc_final: 0.8618 (tppt) REVERT: F 307 GLN cc_start: 0.5072 (OUTLIER) cc_final: 0.4845 (pt0) REVERT: G 345 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8013 (p0) REVERT: H 338 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7857 (tm-30) REVERT: H 358 ASP cc_start: 0.8556 (p0) cc_final: 0.8243 (m-30) REVERT: I 358 ASP cc_start: 0.8726 (p0) cc_final: 0.8394 (m-30) REVERT: J 338 GLU cc_start: 0.7580 (tp30) cc_final: 0.7370 (tp30) REVERT: J 345 ASP cc_start: 0.8589 (t0) cc_final: 0.8214 (t0) outliers start: 30 outliers final: 12 residues processed: 180 average time/residue: 0.5310 time to fit residues: 104.5458 Evaluate side-chains 154 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 378 PHE Chi-restraints excluded: chain F residue 307 GLN Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.113764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.102369 restraints weight = 64566.072| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 6.13 r_work: 0.4354 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5660 Z= 0.210 Angle : 0.660 7.004 7580 Z= 0.335 Chirality : 0.049 0.142 860 Planarity : 0.003 0.025 960 Dihedral : 5.803 20.429 740 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.69 % Allowed : 26.25 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 349 TYR 0.013 0.002 TYR E 310 PHE 0.010 0.001 PHE F 346 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 5660) covalent geometry : angle 0.65985 ( 7580) hydrogen bonds : bond 0.03696 ( 152) hydrogen bonds : angle 5.89045 ( 456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.6030 (pm20) cc_final: 0.5779 (pm20) REVERT: C 350 VAL cc_start: 0.9313 (t) cc_final: 0.8934 (t) REVERT: C 372 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7674 (mp0) REVERT: D 314 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7317 (t0) REVERT: D 337 VAL cc_start: 0.9371 (t) cc_final: 0.9047 (p) REVERT: D 357 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8792 (tm) REVERT: E 351 GLN cc_start: 0.7804 (mt0) cc_final: 0.7459 (mp10) REVERT: H 338 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7582 (tm-30) REVERT: H 358 ASP cc_start: 0.8653 (p0) cc_final: 0.8305 (m-30) REVERT: I 358 ASP cc_start: 0.8735 (p0) cc_final: 0.8519 (m-30) REVERT: J 338 GLU cc_start: 0.7963 (tp30) cc_final: 0.7330 (tm-30) REVERT: J 345 ASP cc_start: 0.8675 (t0) cc_final: 0.8308 (t0) REVERT: J 357 LEU cc_start: 0.8975 (mm) cc_final: 0.8562 (pt) outliers start: 30 outliers final: 17 residues processed: 173 average time/residue: 0.5322 time to fit residues: 100.8243 Evaluate side-chains 159 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 337 VAL Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 327 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.113374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.102150 restraints weight = 64073.159| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 6.11 r_work: 0.4360 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.9118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5660 Z= 0.175 Angle : 0.650 7.376 7580 Z= 0.325 Chirality : 0.049 0.143 860 Planarity : 0.003 0.030 960 Dihedral : 5.656 19.642 740 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.81 % Allowed : 29.69 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.013 0.002 TYR A 310 PHE 0.010 0.001 PHE D 346 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5660) covalent geometry : angle 0.64974 ( 7580) hydrogen bonds : bond 0.03351 ( 152) hydrogen bonds : angle 5.66767 ( 456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 TYR cc_start: 0.8546 (t80) cc_final: 0.8304 (t80) REVERT: A 338 GLU cc_start: 0.5156 (pm20) cc_final: 0.4915 (pm20) REVERT: C 350 VAL cc_start: 0.9303 (t) cc_final: 0.8907 (t) REVERT: C 372 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7777 (mp0) REVERT: D 337 VAL cc_start: 0.9368 (t) cc_final: 0.9013 (p) REVERT: D 357 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8871 (tm) REVERT: E 351 GLN cc_start: 0.7737 (mt0) cc_final: 0.7369 (mp10) REVERT: H 338 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7742 (tm-30) REVERT: H 358 ASP cc_start: 0.8656 (p0) cc_final: 0.8270 (m-30) REVERT: I 358 ASP cc_start: 0.8901 (p0) cc_final: 0.8450 (m-30) REVERT: I 360 ILE cc_start: 0.8205 (mm) cc_final: 0.7832 (mp) REVERT: I 369 LYS cc_start: 0.8629 (mttt) cc_final: 0.8404 (mmmt) REVERT: J 338 GLU cc_start: 0.8010 (tp30) cc_final: 0.7401 (tm-30) REVERT: J 345 ASP cc_start: 0.8702 (t0) cc_final: 0.8286 (t0) REVERT: J 357 LEU cc_start: 0.8945 (mm) cc_final: 0.8572 (pt) outliers start: 18 outliers final: 16 residues processed: 161 average time/residue: 0.4922 time to fit residues: 87.3074 Evaluate side-chains 150 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.115507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.104334 restraints weight = 64005.549| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 6.09 r_work: 0.4414 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.9682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5660 Z= 0.148 Angle : 0.640 6.507 7580 Z= 0.318 Chirality : 0.049 0.151 860 Planarity : 0.003 0.033 960 Dihedral : 5.389 18.041 740 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.97 % Allowed : 31.56 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.018 0.002 TYR E 310 PHE 0.008 0.001 PHE F 346 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5660) covalent geometry : angle 0.64045 ( 7580) hydrogen bonds : bond 0.03022 ( 152) hydrogen bonds : angle 5.39844 ( 456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 372 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8067 (mp0) REVERT: D 337 VAL cc_start: 0.9213 (t) cc_final: 0.8965 (p) REVERT: D 357 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8795 (tm) REVERT: E 372 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: H 338 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7939 (tm-30) REVERT: I 358 ASP cc_start: 0.8665 (p0) cc_final: 0.8362 (m-30) REVERT: I 360 ILE cc_start: 0.8774 (mm) cc_final: 0.8519 (mp) REVERT: J 338 GLU cc_start: 0.7973 (tp30) cc_final: 0.7522 (tm-30) REVERT: J 345 ASP cc_start: 0.8877 (t0) cc_final: 0.8496 (t0) REVERT: J 357 LEU cc_start: 0.8522 (mm) cc_final: 0.8280 (pt) outliers start: 19 outliers final: 9 residues processed: 153 average time/residue: 0.3241 time to fit residues: 57.4937 Evaluate side-chains 143 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 371 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 60 optimal weight: 0.0770 chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 HIS ** G 307 GLN ** 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 = 0.4625 r_free = 0.4625 target = 0.114121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.102731 restraints weight = 62781.901| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 6.08 r_work: 0.4359 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.9960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5660 Z= 0.181 Angle : 0.647 6.304 7580 Z= 0.323 Chirality : 0.049 0.145 860 Planarity : 0.003 0.037 960 Dihedral : 5.431 19.022 740 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 4.38 % Allowed : 31.56 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 349 TYR 0.013 0.002 TYR I 310 PHE 0.010 0.001 PHE D 346 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 5660) covalent geometry : angle 0.64664 ( 7580) hydrogen bonds : bond 0.03078 ( 152) hydrogen bonds : angle 5.31426 ( 456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 ASP cc_start: 0.8473 (t0) cc_final: 0.8084 (p0) REVERT: B 315 LEU cc_start: 0.8967 (pt) cc_final: 0.8630 (pp) REVERT: B 343 LYS cc_start: 0.3729 (OUTLIER) cc_final: 0.3225 (pptt) REVERT: C 372 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8010 (mp0) REVERT: D 357 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8801 (tm) REVERT: E 372 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: H 338 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7650 (tm-30) REVERT: I 358 ASP cc_start: 0.8667 (p0) cc_final: 0.8358 (m-30) REVERT: I 360 ILE cc_start: 0.8333 (mm) cc_final: 0.7977 (mp) REVERT: J 338 GLU cc_start: 0.8258 (tp30) cc_final: 0.7613 (tm-30) REVERT: J 345 ASP cc_start: 0.8650 (t0) cc_final: 0.8245 (t0) REVERT: J 357 LEU cc_start: 0.9038 (mm) cc_final: 0.8459 (pt) outliers start: 28 outliers final: 14 residues processed: 149 average time/residue: 0.3772 time to fit residues: 63.8309 Evaluate side-chains 140 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain I residue 370 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 0.0980 chunk 39 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 5 optimal weight: 0.0470 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** 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 = 0.4651 r_free = 0.4651 target = 0.115563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.104202 restraints weight = 62165.977| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 6.16 r_work: 0.4391 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 1.0065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5660 Z= 0.116 Angle : 0.655 8.111 7580 Z= 0.321 Chirality : 0.051 0.147 860 Planarity : 0.003 0.035 960 Dihedral : 4.980 17.165 740 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.19 % Allowed : 34.06 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.013 0.002 TYR E 310 PHE 0.008 0.001 PHE F 346 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5660) covalent geometry : angle 0.65483 ( 7580) hydrogen bonds : bond 0.02615 ( 152) hydrogen bonds : angle 4.99475 ( 456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 LEU cc_start: 0.9096 (pt) cc_final: 0.8884 (pp) REVERT: B 331 LYS cc_start: 0.3969 (OUTLIER) cc_final: 0.3543 (pptt) REVERT: B 343 LYS cc_start: 0.3684 (OUTLIER) cc_final: 0.3311 (pptt) REVERT: C 357 LEU cc_start: 0.9306 (mp) cc_final: 0.9100 (mm) REVERT: C 372 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8060 (mp0) REVERT: D 337 VAL cc_start: 0.9366 (t) cc_final: 0.9060 (m) REVERT: D 338 GLU cc_start: 0.7863 (tp30) cc_final: 0.7426 (tp30) REVERT: D 357 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8780 (tm) REVERT: E 372 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: F 338 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7529 (tm-30) REVERT: H 314 ASP cc_start: 0.7914 (t0) cc_final: 0.6920 (t0) REVERT: H 338 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7844 (tm-30) REVERT: I 358 ASP cc_start: 0.8671 (p0) cc_final: 0.8389 (m-30) REVERT: I 360 ILE cc_start: 0.8676 (mm) cc_final: 0.8375 (mp) REVERT: J 338 GLU cc_start: 0.8254 (tp30) cc_final: 0.8010 (tp30) REVERT: J 345 ASP cc_start: 0.8606 (t0) cc_final: 0.8208 (t0) REVERT: J 357 LEU cc_start: 0.8945 (mm) cc_final: 0.8276 (pt) outliers start: 14 outliers final: 6 residues processed: 152 average time/residue: 0.3928 time to fit residues: 67.5298 Evaluate side-chains 140 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain H residue 371 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.114215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.102702 restraints weight = 64128.671| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 6.14 r_work: 0.4382 rms_B_bonded: 5.68 restraints_weight: 2.0000 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 1.0327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5660 Z= 0.177 Angle : 0.679 8.739 7580 Z= 0.339 Chirality : 0.049 0.174 860 Planarity : 0.004 0.036 960 Dihedral : 5.144 18.057 740 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.66 % Allowed : 35.16 % Favored : 62.19 % 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: -2.77 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 349 TYR 0.025 0.002 TYR G 310 PHE 0.009 0.001 PHE F 346 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5660) covalent geometry : angle 0.67891 ( 7580) hydrogen bonds : bond 0.02792 ( 152) hydrogen bonds : angle 4.98056 ( 456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.4340 (OUTLIER) cc_final: 0.3834 (pptt) REVERT: C 372 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8164 (mp0) REVERT: D 357 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8698 (tm) REVERT: E 372 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: H 307 GLN cc_start: 0.5895 (OUTLIER) cc_final: 0.5603 (pt0) REVERT: H 338 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7341 (tm-30) REVERT: I 358 ASP cc_start: 0.8683 (p0) cc_final: 0.8458 (m-30) REVERT: I 360 ILE cc_start: 0.8616 (mm) cc_final: 0.8295 (mp) REVERT: J 338 GLU cc_start: 0.8321 (tp30) cc_final: 0.7687 (tm-30) REVERT: J 345 ASP cc_start: 0.8745 (t0) cc_final: 0.8326 (t0) REVERT: J 357 LEU cc_start: 0.8978 (mm) cc_final: 0.8250 (pt) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.3521 time to fit residues: 54.4156 Evaluate side-chains 134 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 370 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.115277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.103574 restraints weight = 63116.347| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 6.16 r_work: 0.4387 rms_B_bonded: 5.67 restraints_weight: 2.0000 r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 1.0386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5660 Z= 0.173 Angle : 0.698 8.142 7580 Z= 0.344 Chirality : 0.050 0.163 860 Planarity : 0.004 0.036 960 Dihedral : 5.134 16.858 740 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.81 % Allowed : 35.31 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 349 TYR 0.022 0.002 TYR G 310 PHE 0.009 0.001 PHE F 346 HIS 0.006 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5660) covalent geometry : angle 0.69764 ( 7580) hydrogen bonds : bond 0.02844 ( 152) hydrogen bonds : angle 4.96354 ( 456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.4165 (OUTLIER) cc_final: 0.3590 (pptt) REVERT: C 372 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8253 (mm-30) REVERT: D 357 LEU cc_start: 0.9116 (mm) cc_final: 0.8748 (tm) REVERT: E 372 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: H 338 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7325 (tm-30) REVERT: I 360 ILE cc_start: 0.8641 (mm) cc_final: 0.8343 (mp) REVERT: J 338 GLU cc_start: 0.8294 (tp30) cc_final: 0.7669 (tm-30) REVERT: J 345 ASP cc_start: 0.8762 (t0) cc_final: 0.8348 (t0) REVERT: J 357 LEU cc_start: 0.8966 (mm) cc_final: 0.8245 (pt) outliers start: 18 outliers final: 9 residues processed: 134 average time/residue: 0.3773 time to fit residues: 57.2671 Evaluate side-chains 130 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 370 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.115550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.104110 restraints weight = 63293.529| |-----------------------------------------------------------------------------| r_work (start): 0.4499 rms_B_bonded: 6.07 r_work: 0.4408 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 1.0518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5660 Z= 0.134 Angle : 0.687 7.668 7580 Z= 0.338 Chirality : 0.051 0.160 860 Planarity : 0.004 0.035 960 Dihedral : 4.915 16.671 740 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.72 % Allowed : 36.41 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.010 0.002 TYR I 310 PHE 0.009 0.001 PHE F 346 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5660) covalent geometry : angle 0.68748 ( 7580) hydrogen bonds : bond 0.02653 ( 152) hydrogen bonds : angle 4.82783 ( 456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3764.06 seconds wall clock time: 64 minutes 42.30 seconds (3882.30 seconds total)