Starting phenix.real_space_refine on Fri Mar 15 13:00:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkh_23894/03_2024/7mkh_23894.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkh_23894/03_2024/7mkh_23894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkh_23894/03_2024/7mkh_23894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkh_23894/03_2024/7mkh_23894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkh_23894/03_2024/7mkh_23894.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkh_23894/03_2024/7mkh_23894.pdb" } resolution = 3.3 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= 0.003 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 3600 2.51 5 N 1060 2.21 5 O 1070 1.98 5 H 5980 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11720 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "I" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "J" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 5.19, per 1000 atoms: 0.44 Number of scatterers: 11720 At special positions: 0 Unit cell: (137.984, 98.098, 47.432, 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 1070 8.00 N 1060 7.00 C 3600 6.00 H 5980 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: 8.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 316 through 320 removed outlier: 6.513A pdb=" N SER A 316 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR C 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER C 316 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR E 319 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER E 316 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR G 319 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER G 316 " --> pdb=" O LYS I 317 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N THR I 319 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL G 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.583A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL E 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS G 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL E 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL G 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS I 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL G 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.386A pdb=" N LEU A 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS C 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE A 346 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS E 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE C 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU E 344 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LYS G 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE E 346 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU G 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS I 347 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE G 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.910A pdb=" N SER A 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER C 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER E 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER G 356 " --> pdb=" O GLY I 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.309A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR E 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR G 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 367 through 376 Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.343A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL F 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE D 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL F 306 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL H 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE F 308 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL H 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL J 309 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE H 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 316 through 324 removed outlier: 6.413A pdb=" N SER B 316 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR D 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY D 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER D 316 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR F 319 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LYS F 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY F 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS D 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER F 316 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR H 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL F 318 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LYS H 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER F 320 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY H 323 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS F 322 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER H 316 " --> pdb=" O LYS J 317 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR J 319 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL H 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LYS J 321 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER H 320 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY J 323 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS H 322 " --> pdb=" O GLY J 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.564A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LYS H 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL F 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL H 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LYS J 340 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL H 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 343 through 347 Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 356 removed outlier: 6.901A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER D 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER F 356 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER H 356 " --> pdb=" O GLY J 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.309A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR H 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 367 through 378 160 hydrogen bonds defined for protein. 480 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: 3.93 Time building geometry restraints manager: 9.20 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: 5970 1.12 - 1.30: 961 1.30 - 1.47: 2344 1.47 - 1.64: 2525 1.64 - 1.82: 10 Bond restraints: 11810 Sorted by residual: bond pdb=" NE2 HIS G 374 " pdb=" HE2 HIS G 374 " ideal model delta sigma weight residual 0.860 1.049 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" NE2 HIS E 374 " pdb=" HE2 HIS E 374 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" NE2 HIS I 374 " pdb=" HE2 HIS I 374 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" NE2 HIS A 374 " pdb=" HE2 HIS A 374 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" NE2 HIS C 374 " pdb=" HE2 HIS C 374 " ideal model delta sigma weight residual 0.860 1.048 -0.188 2.00e-02 2.50e+03 8.81e+01 ... (remaining 11805 not shown) Histogram of bond angle deviations from ideal: 93.73 - 101.73: 30 101.73 - 109.73: 10606 109.73 - 117.73: 5835 117.73 - 125.73: 4853 125.73 - 133.73: 196 Bond angle restraints: 21520 Sorted by residual: angle pdb=" CA PHE E 378 " pdb=" CB PHE E 378 " pdb=" CG PHE E 378 " ideal model delta sigma weight residual 113.80 120.69 -6.89 1.00e+00 1.00e+00 4.75e+01 angle pdb=" CA PHE G 378 " pdb=" CB PHE G 378 " pdb=" CG PHE G 378 " ideal model delta sigma weight residual 113.80 120.69 -6.89 1.00e+00 1.00e+00 4.74e+01 angle pdb=" CA PHE C 378 " pdb=" CB PHE C 378 " pdb=" CG PHE C 378 " ideal model delta sigma weight residual 113.80 120.68 -6.88 1.00e+00 1.00e+00 4.74e+01 angle pdb=" CA PHE I 378 " pdb=" CB PHE I 378 " pdb=" CG PHE I 378 " ideal model delta sigma weight residual 113.80 120.68 -6.88 1.00e+00 1.00e+00 4.74e+01 angle pdb=" CA PHE A 378 " pdb=" CB PHE A 378 " pdb=" CG PHE A 378 " ideal model delta sigma weight residual 113.80 120.68 -6.88 1.00e+00 1.00e+00 4.73e+01 ... (remaining 21515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.32: 5040 13.32 - 26.64: 190 26.64 - 39.97: 95 39.97 - 53.29: 70 53.29 - 66.61: 45 Dihedral angle restraints: 5440 sinusoidal: 3110 harmonic: 2330 Sorted by residual: dihedral pdb=" CD2 HIS F 330 " pdb=" CG HIS F 330 " pdb=" ND1 HIS F 330 " pdb=" HD1 HIS F 330 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CD2 HIS J 330 " pdb=" CG HIS J 330 " pdb=" ND1 HIS J 330 " pdb=" HD1 HIS J 330 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CD2 HIS D 330 " pdb=" CG HIS D 330 " pdb=" ND1 HIS D 330 " pdb=" HD1 HIS D 330 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 458 0.068 - 0.135: 284 0.135 - 0.203: 113 0.203 - 0.271: 20 0.271 - 0.338: 5 Chirality restraints: 880 Sorted by residual: chirality pdb=" CA PHE D 346 " pdb=" N PHE D 346 " pdb=" C PHE D 346 " pdb=" CB PHE D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA PHE F 346 " pdb=" N PHE F 346 " pdb=" C PHE F 346 " pdb=" CB PHE F 346 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA PHE J 346 " pdb=" N PHE J 346 " pdb=" C PHE J 346 " pdb=" CB PHE J 346 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 877 not shown) Planarity restraints: 1700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS J 330 " -0.049 2.00e-02 2.50e+03 6.21e-02 8.68e+01 pdb=" CG HIS J 330 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS J 330 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 HIS J 330 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS J 330 " -0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS J 330 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 HIS J 330 " 0.143 2.00e-02 2.50e+03 pdb=" HD2 HIS J 330 " 0.055 2.00e-02 2.50e+03 pdb=" HE1 HIS J 330 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 330 " -0.049 2.00e-02 2.50e+03 6.21e-02 8.68e+01 pdb=" CG HIS F 330 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS F 330 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 HIS F 330 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS F 330 " -0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS F 330 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 HIS F 330 " 0.143 2.00e-02 2.50e+03 pdb=" HD2 HIS F 330 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 HIS F 330 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 330 " -0.049 2.00e-02 2.50e+03 6.21e-02 8.66e+01 pdb=" CG HIS D 330 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS D 330 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 HIS D 330 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS D 330 " -0.029 2.00e-02 2.50e+03 pdb=" NE2 HIS D 330 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 HIS D 330 " 0.143 2.00e-02 2.50e+03 pdb=" HD2 HIS D 330 " 0.055 2.00e-02 2.50e+03 pdb=" HE1 HIS D 330 " -0.039 2.00e-02 2.50e+03 ... (remaining 1697 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1161 2.18 - 2.79: 22392 2.79 - 3.39: 30288 3.39 - 4.00: 42645 4.00 - 4.60: 61443 Nonbonded interactions: 157929 Sorted by model distance: nonbonded pdb=" HD1 HIS D 330 " pdb=" OG1 THR D 361 " model vdw 1.580 1.850 nonbonded pdb=" HD1 HIS B 330 " pdb=" OG1 THR B 361 " model vdw 1.581 1.850 nonbonded pdb=" HD1 HIS J 330 " pdb=" OG1 THR J 361 " model vdw 1.581 1.850 nonbonded pdb=" HD1 HIS H 330 " pdb=" OG1 THR H 361 " model vdw 1.581 1.850 nonbonded pdb=" HD1 HIS F 330 " pdb=" OG1 THR F 361 " model vdw 1.581 1.850 ... (remaining 157924 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: 1.350 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: 0.170 Extract box with map and model: 7.020 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.310 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 : 0.023 0.190 5830 Z= 1.540 Angle : 1.991 9.386 7800 Z= 1.304 Chirality : 0.097 0.338 880 Planarity : 0.009 0.030 990 Dihedral : 8.929 66.609 2240 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS H 362 PHE 0.030 0.007 PHE E 378 TYR 0.026 0.010 TYR F 310 ARG 0.002 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0 residues processed: 169 average time/residue: 0.5904 time to fit residues: 119.6187 Evaluate side-chains 83 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5830 Z= 0.337 Angle : 0.757 8.694 7800 Z= 0.413 Chirality : 0.052 0.156 880 Planarity : 0.004 0.033 990 Dihedral : 5.588 19.044 770 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 1.67 % Allowed : 9.39 % Favored : 88.94 % 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: -2.57 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 329 PHE 0.017 0.002 PHE D 346 TYR 0.008 0.002 TYR I 310 ARG 0.006 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.007 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: B 378 PHE cc_start: 0.6699 (t80) cc_final: 0.6413 (t80) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.4281 time to fit residues: 52.9349 Evaluate side-chains 69 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 314 ASP Chi-restraints excluded: chain I residue 358 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5830 Z= 0.210 Angle : 0.632 6.242 7800 Z= 0.340 Chirality : 0.051 0.137 880 Planarity : 0.003 0.026 990 Dihedral : 5.163 16.205 770 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.52 % Allowed : 11.82 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.66 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 374 PHE 0.012 0.001 PHE I 378 TYR 0.007 0.002 TYR H 310 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.3831 time to fit residues: 34.8272 Evaluate side-chains 61 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5830 Z= 0.235 Angle : 0.592 5.645 7800 Z= 0.316 Chirality : 0.050 0.130 880 Planarity : 0.003 0.026 990 Dihedral : 5.109 15.830 770 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.12 % Allowed : 10.45 % Favored : 87.42 % 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: -2.76 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 329 PHE 0.008 0.001 PHE A 378 TYR 0.007 0.002 TYR B 310 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 357 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6818 (mt) outliers start: 14 outliers final: 12 residues processed: 59 average time/residue: 0.3232 time to fit residues: 26.6200 Evaluate side-chains 56 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 358 ASP Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 346 PHE 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: 0.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5830 Z= 0.257 Angle : 0.575 5.426 7800 Z= 0.305 Chirality : 0.049 0.131 880 Planarity : 0.003 0.023 990 Dihedral : 5.148 16.041 770 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.88 % Allowed : 10.30 % Favored : 86.82 % 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: -2.93 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 329 PHE 0.008 0.001 PHE F 346 TYR 0.006 0.002 TYR B 310 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 18 residues processed: 48 average time/residue: 0.3244 time to fit residues: 22.0503 Evaluate side-chains 52 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 34 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 358 ASP Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 346 PHE Chi-restraints excluded: chain J residue 357 LEU 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: 9.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5830 Z= 0.407 Angle : 0.685 5.979 7800 Z= 0.370 Chirality : 0.050 0.144 880 Planarity : 0.004 0.026 990 Dihedral : 6.081 17.657 770 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 3.94 % Allowed : 10.30 % Favored : 85.76 % 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: -3.29 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 329 PHE 0.017 0.002 PHE B 378 TYR 0.007 0.002 TYR D 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 23 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 346 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7213 (p90) outliers start: 26 outliers final: 23 residues processed: 41 average time/residue: 0.3324 time to fit residues: 19.7062 Evaluate side-chains 46 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 22 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 358 ASP Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 346 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS C 329 HIS ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS G 329 HIS ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.7721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5830 Z= 0.374 Angle : 0.640 5.739 7800 Z= 0.343 Chirality : 0.049 0.143 880 Planarity : 0.004 0.028 990 Dihedral : 5.930 17.595 770 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 3.79 % Allowed : 11.67 % Favored : 84.55 % 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: -3.52 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 329 PHE 0.012 0.002 PHE F 346 TYR 0.007 0.002 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 24 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 346 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7073 (p90) outliers start: 25 outliers final: 21 residues processed: 39 average time/residue: 0.3124 time to fit residues: 17.6994 Evaluate side-chains 46 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 24 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 358 ASP Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 346 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 chunk 53 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.7731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5830 Z= 0.173 Angle : 0.523 5.131 7800 Z= 0.277 Chirality : 0.050 0.128 880 Planarity : 0.003 0.027 990 Dihedral : 5.128 15.579 770 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.42 % Allowed : 12.73 % Favored : 84.85 % 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: -3.46 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.009 0.001 PHE A 378 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 28 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 313 VAL cc_start: 0.8263 (t) cc_final: 0.8050 (p) outliers start: 16 outliers final: 16 residues processed: 39 average time/residue: 0.3156 time to fit residues: 17.7571 Evaluate side-chains 42 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 26 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 358 ASP Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 346 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.7957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5830 Z= 0.349 Angle : 0.604 5.682 7800 Z= 0.321 Chirality : 0.049 0.144 880 Planarity : 0.003 0.027 990 Dihedral : 5.527 16.916 770 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.58 % Allowed : 13.48 % Favored : 83.94 % 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: -3.66 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS A 329 PHE 0.011 0.002 PHE G 378 TYR 0.006 0.002 TYR D 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 22 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 346 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7140 (p90) outliers start: 17 outliers final: 14 residues processed: 33 average time/residue: 0.3015 time to fit residues: 14.9055 Evaluate side-chains 36 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 21 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 346 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5830 Z= 0.273 Angle : 0.564 5.338 7800 Z= 0.299 Chirality : 0.049 0.131 880 Planarity : 0.003 0.028 990 Dihedral : 5.393 16.301 770 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % Favored : 84.09 % 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: -3.76 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.17), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 329 PHE 0.010 0.002 PHE A 378 TYR 0.006 0.002 TYR A 310 ARG 0.002 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 23 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 346 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7113 (p90) outliers start: 15 outliers final: 14 residues processed: 32 average time/residue: 0.2747 time to fit residues: 13.7493 Evaluate side-chains 36 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 21 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 346 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.082306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.071266 restraints weight = 77982.749| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 6.31 r_work: 0.4009 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.8169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5830 Z= 0.181 Angle : 0.517 5.304 7800 Z= 0.273 Chirality : 0.050 0.130 880 Planarity : 0.003 0.029 990 Dihedral : 4.996 15.225 770 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.27 % Allowed : 13.94 % Favored : 83.79 % 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: -3.70 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.17), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.014 0.001 PHE A 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.16 seconds wall clock time: 52 minutes 13.44 seconds (3133.44 seconds total)