Starting phenix.real_space_refine on Sun Dec 29 20:23:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkf_23871/12_2024/7mkf_23871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkf_23871/12_2024/7mkf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mkf_23871/12_2024/7mkf_23871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkf_23871/12_2024/7mkf_23871.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkf_23871/12_2024/7mkf_23871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkf_23871/12_2024/7mkf_23871.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.05, per 1000 atoms: 0.53 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: 2.99 Conformation dependent library (CDL) restraints added in 806.4 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: 1.22 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: 4.49 Time building geometry restraints manager: 3.52 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: 1.340 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: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.820 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- 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= 1.513 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.007 0.003 HIS J 374 PHE 0.025 0.006 PHE D 346 TYR 0.017 0.006 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** 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 : 0.958 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 outliers start: 0 outliers final: 1 residues processed: 282 average time/residue: 2.0608 time to fit residues: 612.6255 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 : 0.975 ------------------------------------------------------------------------------- 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 59 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.6906 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= 0.317 Angle : 0.741 5.762 7580 Z= 0.386 Chirality : 0.050 0.170 860 Planarity : 0.004 0.038 960 Dihedral : 5.860 19.388 742 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.62 % Allowed : 22.34 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (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 HIS 0.006 0.001 HIS G 330 PHE 0.012 0.002 PHE F 346 TYR 0.011 0.002 TYR D 310 ARG 0.007 0.001 ARG D 349 *********************** 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: 36 poor density : 167 time to evaluate : 1.021 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: A 309 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7319 (p) REVERT: J 307 GLN cc_start: 0.5180 (OUTLIER) cc_final: 0.4535 (mm-40) outliers start: 36 outliers final: 16 residues processed: 193 average time/residue: 1.0028 time to fit residues: 216.3709 Evaluate side-chains 152 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL 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 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 35 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.8134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5660 Z= 0.315 Angle : 0.694 5.585 7580 Z= 0.355 Chirality : 0.049 0.152 860 Planarity : 0.003 0.019 960 Dihedral : 5.867 20.318 740 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.00 % Allowed : 26.25 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 374 PHE 0.014 0.001 PHE F 346 TYR 0.010 0.002 TYR D 310 ARG 0.004 0.001 ARG D 349 *********************** 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 181 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.905 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: A 309 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7317 (p) outliers start: 32 outliers final: 11 residues processed: 174 average time/residue: 1.1751 time to fit residues: 223.5823 Evaluate side-chains 145 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain D residue 313 VAL 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 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 J residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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** F 362 HIS ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.8918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5660 Z= 0.236 Angle : 0.660 7.328 7580 Z= 0.327 Chirality : 0.050 0.148 860 Planarity : 0.003 0.023 960 Dihedral : 5.596 21.125 740 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.59 % Allowed : 28.59 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.005 0.001 HIS F 374 PHE 0.009 0.001 PHE D 346 TYR 0.013 0.002 TYR E 310 ARG 0.003 0.001 ARG B 349 *********************** 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 170 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.059 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: A 309 VAL cc_start: 0.7473 (OUTLIER) cc_final: 0.7218 (p) outliers start: 23 outliers final: 10 residues processed: 159 average time/residue: 1.0358 time to fit residues: 183.2858 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 : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL 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 337 VAL Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.9467 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= 0.283 Angle : 0.652 6.258 7580 Z= 0.327 Chirality : 0.049 0.144 860 Planarity : 0.003 0.030 960 Dihedral : 5.589 18.823 740 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.75 % Allowed : 29.69 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 374 PHE 0.009 0.001 PHE F 346 TYR 0.014 0.002 TYR A 310 ARG 0.002 0.001 ARG B 349 *********************** 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 161 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.095 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: A 309 VAL cc_start: 0.7489 (OUTLIER) cc_final: 0.7264 (p) outliers start: 24 outliers final: 18 residues processed: 153 average time/residue: 1.0053 time to fit residues: 170.7882 Evaluate side-chains 145 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL 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 337 VAL 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 313 VAL Chi-restraints excluded: chain D residue 371 ILE 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 344 LEU Chi-restraints excluded: chain J residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.9950 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= 0.231 Angle : 0.655 8.018 7580 Z= 0.323 Chirality : 0.050 0.147 860 Planarity : 0.003 0.032 960 Dihedral : 5.347 17.331 740 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.28 % Allowed : 31.72 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.008 0.001 PHE F 346 TYR 0.020 0.002 TYR A 310 ARG 0.003 0.000 ARG B 349 *********************** 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 158 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.035 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: A 309 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7259 (p) REVERT: B 315 LEU cc_start: 0.7703 (pt) cc_final: 0.7398 (pp) REVERT: B 343 LYS cc_start: 0.4585 (OUTLIER) cc_final: 0.3946 (pptt) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 1.0110 time to fit residues: 171.2128 Evaluate side-chains 138 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 371 ILE 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 344 LEU Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 1.0269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5660 Z= 0.331 Angle : 0.683 6.781 7580 Z= 0.346 Chirality : 0.049 0.150 860 Planarity : 0.004 0.038 960 Dihedral : 5.614 19.451 740 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.59 % Allowed : 32.97 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 374 PHE 0.011 0.001 PHE C 378 TYR 0.016 0.002 TYR A 310 ARG 0.002 0.000 ARG I 349 *********************** 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 143 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.972 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: A 309 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7282 (p) REVERT: B 315 LEU cc_start: 0.7650 (pt) cc_final: 0.7273 (pp) outliers start: 23 outliers final: 14 residues processed: 138 average time/residue: 0.8039 time to fit residues: 126.6238 Evaluate side-chains 127 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 320 SER 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 344 LEU Chi-restraints excluded: chain J residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** H 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 1.0584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5660 Z= 0.345 Angle : 0.708 7.042 7580 Z= 0.357 Chirality : 0.049 0.167 860 Planarity : 0.004 0.041 960 Dihedral : 5.786 23.441 740 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.53 % Allowed : 33.12 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 374 PHE 0.011 0.002 PHE C 378 TYR 0.013 0.002 TYR A 310 ARG 0.003 0.000 ARG I 349 *********************** 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 143 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.859 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: A 309 VAL cc_start: 0.7573 (OUTLIER) cc_final: 0.7340 (p) REVERT: B 343 LYS cc_start: 0.4919 (OUTLIER) cc_final: 0.3907 (pptt) outliers start: 29 outliers final: 21 residues processed: 134 average time/residue: 0.6830 time to fit residues: 106.5846 Evaluate side-chains 134 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL 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 343 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C 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 371 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 344 LEU 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 H residue 376 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain J residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 1.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5660 Z= 0.242 Angle : 0.691 7.701 7580 Z= 0.341 Chirality : 0.050 0.152 860 Planarity : 0.004 0.038 960 Dihedral : 5.375 19.464 740 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.81 % Allowed : 35.62 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.011 0.001 PHE D 346 TYR 0.011 0.002 TYR A 310 ARG 0.003 0.000 ARG D 349 *********************** 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 136 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.012 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: A 309 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7309 (p) REVERT: B 343 LYS cc_start: 0.4796 (OUTLIER) cc_final: 0.3823 (pptt) REVERT: I 358 ASP cc_start: 0.5070 (OUTLIER) cc_final: 0.4739 (m-30) outliers start: 18 outliers final: 17 residues processed: 131 average time/residue: 0.6739 time to fit residues: 103.1840 Evaluate side-chains 129 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL 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 343 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain H residue 371 ILE Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 1.0753 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= 0.274 Angle : 0.704 7.087 7580 Z= 0.348 Chirality : 0.050 0.154 860 Planarity : 0.004 0.038 960 Dihedral : 5.355 19.879 740 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.12 % Allowed : 35.47 % Favored : 61.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 374 PHE 0.009 0.001 PHE F 346 TYR 0.011 0.002 TYR A 310 ARG 0.002 0.000 ARG J 349 ********************** 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 132 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.886 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: A 309 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7317 (p) outliers start: 20 outliers final: 16 residues processed: 129 average time/residue: 0.6527 time to fit residues: 98.9526 Evaluate side-chains 126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL 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 356 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 320 SER 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 H residue 376 LEU Chi-restraints excluded: chain I residue 325 LEU Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain J residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.4639 r_free = 0.4639 target = 0.114605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.103213 restraints weight = 62346.981| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 6.22 r_work: 0.4381 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 1.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5660 Z= 0.224 Angle : 0.696 7.820 7580 Z= 0.341 Chirality : 0.051 0.155 860 Planarity : 0.004 0.037 960 Dihedral : 5.114 18.465 740 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.03 % Allowed : 36.72 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 374 PHE 0.009 0.001 PHE F 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4455.63 seconds wall clock time: 80 minutes 25.80 seconds (4825.80 seconds total)