Starting phenix.real_space_refine on Fri Mar 15 10:12:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkf_23871/03_2024/7mkf_23871.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkf_23871/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkf_23871/03_2024/7mkf_23871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkf_23871/03_2024/7mkf_23871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkf_23871/03_2024/7mkf_23871.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkf_23871/03_2024/7mkf_23871.pdb" } 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 Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.39, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 10.05 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.28 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: 4.37 Time building geometry restraints manager: 10.43 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: 93.39 - 101.50: 30 101.50 - 109.61: 9783 109.61 - 117.72: 6197 117.72 - 125.82: 4717 125.82 - 133.93: 183 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 1.850 nonbonded pdb=" HZ1 LYS A 353 " pdb=" OD2 ASP A 358 " model vdw 1.615 1.850 nonbonded pdb=" HZ1 LYS I 353 " pdb=" OD2 ASP I 358 " model vdw 1.616 1.850 nonbonded pdb=" HZ1 LYS G 353 " pdb=" OD2 ASP G 358 " model vdw 1.616 1.850 nonbonded pdb=" HZ1 LYS C 353 " pdb=" OD2 ASP C 358 " model vdw 1.616 1.850 ... (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 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 6.120 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 42.270 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:14.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.970 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 0.960 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: 1.9574 time to fit residues: 581.3778 Evaluate side-chains 128 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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: 5.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS E 362 HIS G 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 5660 Z= 0.318 Angle : 0.742 5.621 7580 Z= 0.386 Chirality : 0.049 0.173 860 Planarity : 0.004 0.038 960 Dihedral : 5.659 19.214 742 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 7.97 % Allowed : 21.56 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 330 PHE 0.013 0.002 PHE F 346 TYR 0.010 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 216 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 165 time to evaluate : 1.123 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: 0.7592 (OUTLIER) cc_final: 0.7334 (p) outliers start: 51 outliers final: 24 residues processed: 200 average time/residue: 0.9915 time to fit residues: 219.8466 Evaluate side-chains 155 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 353 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 320 SER Chi-restraints excluded: chain H residue 358 ASP 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 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.7906 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= 0.243 Angle : 0.685 7.594 7580 Z= 0.348 Chirality : 0.050 0.258 860 Planarity : 0.003 0.023 960 Dihedral : 5.465 16.730 740 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 5.47 % Allowed : 27.19 % Favored : 67.34 % 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: -2.42 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 374 PHE 0.009 0.001 PHE F 346 TYR 0.011 0.002 TYR E 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 188 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 0.884 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: 0.7524 (OUTLIER) cc_final: 0.7270 (p) outliers start: 35 outliers final: 18 residues processed: 178 average time/residue: 1.0488 time to fit residues: 205.6492 Evaluate side-chains 145 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 376 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 358 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 Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 358 ASP 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: 10.0000 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 0.0870 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.8626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5660 Z= 0.233 Angle : 0.640 5.918 7580 Z= 0.318 Chirality : 0.049 0.148 860 Planarity : 0.003 0.025 960 Dihedral : 5.329 18.910 740 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.00 % Allowed : 29.22 % Favored : 65.78 % 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 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.009 0.001 PHE F 346 TYR 0.014 0.002 TYR E 310 ARG 0.003 0.000 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 171 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.082 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: 0.7484 (OUTLIER) cc_final: 0.7232 (p) outliers start: 32 outliers final: 19 residues processed: 161 average time/residue: 0.8615 time to fit residues: 155.9231 Evaluate side-chains 148 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 C residue 320 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 307 GLN 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 320 SER 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: 20.0000 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 overall best weight: 5.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.9167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5660 Z= 0.298 Angle : 0.654 7.612 7580 Z= 0.329 Chirality : 0.048 0.145 860 Planarity : 0.003 0.029 960 Dihedral : 5.529 19.087 740 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 5.78 % Allowed : 29.38 % Favored : 64.84 % 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: -2.71 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 374 PHE 0.009 0.001 PHE H 346 TYR 0.015 0.002 TYR E 310 ARG 0.003 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 167 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.038 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: 0.7549 (OUTLIER) cc_final: 0.7340 (p) REVERT: B 343 LYS cc_start: 0.4789 (OUTLIER) cc_final: 0.4148 (pptt) REVERT: E 345 ASP cc_start: 0.5551 (t0) cc_final: 0.5221 (t0) outliers start: 37 outliers final: 20 residues processed: 159 average time/residue: 1.0728 time to fit residues: 187.8030 Evaluate side-chains 142 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 343 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 358 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 Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain I residue 370 LYS 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: 9.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.9595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5660 Z= 0.278 Angle : 0.651 7.727 7580 Z= 0.325 Chirality : 0.048 0.151 860 Planarity : 0.004 0.029 960 Dihedral : 5.412 18.178 740 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 5.16 % Allowed : 31.25 % Favored : 63.59 % 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: -2.78 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 374 PHE 0.009 0.001 PHE F 346 TYR 0.012 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 155 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 0.863 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: 0.7579 (OUTLIER) cc_final: 0.7351 (p) REVERT: B 315 LEU cc_start: 0.7642 (pt) cc_final: 0.7318 (pp) outliers start: 33 outliers final: 24 residues processed: 145 average time/residue: 0.8916 time to fit residues: 144.6953 Evaluate side-chains 137 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 311 LYS 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 320 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 315 LEU 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 E residue 358 ASP Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 336 GLN Chi-restraints excluded: chain H residue 338 GLU 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 I residue 370 LYS Chi-restraints excluded: chain J residue 320 SER 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: 0.4980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 0.0370 overall best weight: 2.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.9842 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= 0.206 Angle : 0.637 7.239 7580 Z= 0.315 Chirality : 0.050 0.153 860 Planarity : 0.003 0.029 960 Dihedral : 5.009 15.868 740 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.53 % Allowed : 31.88 % Favored : 63.59 % 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: -2.73 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.009 0.001 PHE D 346 TYR 0.011 0.002 TYR A 310 ARG 0.002 0.000 ARG B 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 154 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.005 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 309 VAL cc_start: 0.7489 (OUTLIER) cc_final: 0.7266 (p) REVERT: A 353 LYS cc_start: 0.5336 (OUTLIER) cc_final: 0.5099 (pptt) outliers start: 29 outliers final: 20 residues processed: 144 average time/residue: 0.8338 time to fit residues: 136.0265 Evaluate side-chains 138 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 353 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 371 ILE 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 I residue 370 LYS 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: 10.0000 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 1.0226 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= 0.332 Angle : 0.674 6.771 7580 Z= 0.339 Chirality : 0.048 0.146 860 Planarity : 0.004 0.030 960 Dihedral : 5.467 17.189 740 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.00 % Allowed : 32.19 % Favored : 62.81 % 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: -2.96 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 374 PHE 0.012 0.001 PHE C 378 TYR 0.013 0.002 TYR E 310 ARG 0.003 0.001 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 fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.047 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: 0.7534 (OUTLIER) cc_final: 0.7318 (p) REVERT: A 353 LYS cc_start: 0.5497 (OUTLIER) cc_final: 0.5251 (pptt) REVERT: H 338 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6197 (tp30) outliers start: 32 outliers final: 23 residues processed: 133 average time/residue: 0.8263 time to fit residues: 124.9099 Evaluate side-chains 135 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 353 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 337 VAL 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 E residue 358 ASP Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 371 ILE 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 I residue 370 LYS 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: 1.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 1.0343 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= 0.246 Angle : 0.654 7.044 7580 Z= 0.324 Chirality : 0.049 0.147 860 Planarity : 0.004 0.031 960 Dihedral : 5.180 17.919 740 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.22 % Allowed : 33.59 % 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 (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: -2.97 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.009 0.001 PHE F 346 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG I 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 142 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.061 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: 0.7626 (OUTLIER) cc_final: 0.7394 (p) REVERT: A 353 LYS cc_start: 0.5391 (OUTLIER) cc_final: 0.5171 (pptt) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.8348 time to fit residues: 124.7695 Evaluate side-chains 133 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 353 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 358 ASP 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 I residue 370 LYS 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 69 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 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 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 1.0575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5660 Z= 0.302 Angle : 0.693 8.506 7580 Z= 0.345 Chirality : 0.049 0.135 860 Planarity : 0.004 0.030 960 Dihedral : 5.291 18.637 740 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.06 % Allowed : 33.91 % Favored : 62.03 % 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: -3.05 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 374 PHE 0.010 0.001 PHE C 378 TYR 0.012 0.002 TYR A 310 ARG 0.002 0.001 ARG I 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 135 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 1.060 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: 0.7599 (OUTLIER) cc_final: 0.7360 (p) REVERT: A 353 LYS cc_start: 0.5527 (OUTLIER) cc_final: 0.5195 (pptt) outliers start: 26 outliers final: 21 residues processed: 126 average time/residue: 0.7357 time to fit residues: 106.9836 Evaluate side-chains 127 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 353 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 358 ASP 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 I residue 370 LYS 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: 20.0000 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.112946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.101934 restraints weight = 66287.635| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 6.08 r_work: 0.4363 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 1.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5660 Z= 0.313 Angle : 0.697 8.567 7580 Z= 0.347 Chirality : 0.049 0.155 860 Planarity : 0.004 0.032 960 Dihedral : 5.377 19.015 740 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 25.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.91 % Allowed : 34.22 % 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 (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: -3.09 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 374 PHE 0.011 0.001 PHE C 378 TYR 0.013 0.002 TYR A 310 ARG 0.003 0.001 ARG I 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4498.07 seconds wall clock time: 79 minutes 32.88 seconds (4772.88 seconds total)