Starting phenix.real_space_refine on Tue Jul 29 20:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkh_23894/07_2025/7mkh_23894.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkh_23894/07_2025/7mkh_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/cci-nas-00/data/ceres_data/7mkh_23894/07_2025/7mkh_23894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkh_23894/07_2025/7mkh_23894.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkh_23894/07_2025/7mkh_23894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkh_23894/07_2025/7mkh_23894.cif" } 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. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.41, per 1000 atoms: 0.55 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 778.9 milliseconds 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: 1.23 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: 4.18 Time building geometry restraints manager: 3.66 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: 0.00 - 3.06: 18744 3.06 - 6.11: 1925 6.11 - 9.16: 741 9.16 - 12.22: 105 12.22 - 15.27: 5 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 2.450 nonbonded pdb=" HD1 HIS B 330 " pdb=" OG1 THR B 361 " model vdw 1.581 2.450 nonbonded pdb=" HD1 HIS J 330 " pdb=" OG1 THR J 361 " model vdw 1.581 2.450 nonbonded pdb=" HD1 HIS H 330 " pdb=" OG1 THR H 361 " model vdw 1.581 2.450 nonbonded pdb=" HD1 HIS F 330 " pdb=" OG1 THR F 361 " model vdw 1.581 2.450 ... (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 Time spend for trying shortcut: 0.01 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: 2.040 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: 0.200 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.730 Find NCS groups from input model: 0.320 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- 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= 1.254 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 Details of bonding type rmsd hydrogen bonds : bond 0.13765 ( 160) hydrogen bonds : angle 10.29374 ( 480) covalent geometry : bond 0.02259 ( 5830) covalent geometry : angle 1.99092 ( 7800) *********************** 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 to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.923 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: 0.5755 time to fit residues: 116.1609 Evaluate side-chains 83 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.088224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.076181 restraints weight = 72164.885| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 6.95 r_work: 0.4081 rms_B_bonded: 6.04 restraints_weight: 2.0000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5830 Z= 0.241 Angle : 0.757 8.749 7800 Z= 0.411 Chirality : 0.054 0.155 880 Planarity : 0.005 0.034 990 Dihedral : 5.733 19.384 770 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.06 % Allowed : 9.39 % Favored : 89.55 % 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: -2.39 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 329 PHE 0.017 0.002 PHE D 346 TYR 0.008 0.002 TYR B 310 ARG 0.006 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.06030 ( 160) hydrogen bonds : angle 7.08319 ( 480) covalent geometry : bond 0.00504 ( 5830) covalent geometry : angle 0.75659 ( 7800) *********************** 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 100 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.073 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: A 348 ASP cc_start: 0.8535 (t0) cc_final: 0.8277 (m-30) REVERT: B 358 ASP cc_start: 0.8708 (p0) cc_final: 0.8322 (m-30) REVERT: C 348 ASP cc_start: 0.8058 (t0) cc_final: 0.7737 (m-30) REVERT: D 340 LYS cc_start: 0.9165 (tttt) cc_final: 0.8957 (tptp) REVERT: D 372 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8328 (mp0) REVERT: D 378 PHE cc_start: 0.8666 (t80) cc_final: 0.8432 (t80) REVERT: E 348 ASP cc_start: 0.8265 (t0) cc_final: 0.8011 (m-30) REVERT: G 348 ASP cc_start: 0.7716 (t0) cc_final: 0.7406 (m-30) REVERT: I 351 GLN cc_start: 0.7470 (tt0) cc_final: 0.7150 (tm-30) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.4473 time to fit residues: 54.0648 Evaluate side-chains 76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain D residue 314 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.086494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.074749 restraints weight = 73033.354| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 6.63 r_work: 0.4140 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5830 Z= 0.231 Angle : 0.702 6.292 7800 Z= 0.379 Chirality : 0.051 0.138 880 Planarity : 0.004 0.021 990 Dihedral : 5.667 19.212 770 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.12 % Allowed : 10.30 % Favored : 87.58 % 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 : -2.09 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 329 PHE 0.010 0.002 PHE I 378 TYR 0.010 0.003 TYR E 310 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.05328 ( 160) hydrogen bonds : angle 6.40347 ( 480) covalent geometry : bond 0.00474 ( 5830) covalent geometry : angle 0.70180 ( 7800) *********************** 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 81 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 1.086 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: B 378 PHE cc_start: 0.8518 (t80) cc_final: 0.7998 (t80) REVERT: C 372 GLU cc_start: 0.7108 (mp0) cc_final: 0.6854 (mp0) REVERT: D 372 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8426 (mp0) REVERT: G 340 LYS cc_start: 0.7324 (mttt) cc_final: 0.7067 (tptp) REVERT: H 378 PHE cc_start: 0.8596 (t80) cc_final: 0.8340 (t80) REVERT: I 351 GLN cc_start: 0.7757 (tt0) cc_final: 0.7327 (tm-30) REVERT: J 308 ILE cc_start: 0.8600 (pt) cc_final: 0.8249 (mp) outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 0.4201 time to fit residues: 38.8500 Evaluate side-chains 65 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 357 LEU 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 J residue 346 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.085850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.074277 restraints weight = 74348.252| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 6.50 r_work: 0.4078 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5830 Z= 0.157 Angle : 0.592 5.527 7800 Z= 0.315 Chirality : 0.050 0.131 880 Planarity : 0.003 0.022 990 Dihedral : 5.276 17.600 770 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.91 % Allowed : 11.06 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.007 0.001 PHE I 378 TYR 0.007 0.002 TYR C 310 ARG 0.003 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 160) hydrogen bonds : angle 5.89247 ( 480) covalent geometry : bond 0.00320 ( 5830) covalent geometry : angle 0.59240 ( 7800) *********************** 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 67 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 1.025 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 375 LYS cc_start: 0.8848 (tttt) cc_final: 0.8517 (tmtt) REVERT: B 378 PHE cc_start: 0.8467 (t80) cc_final: 0.7963 (t80) REVERT: D 372 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8383 (mp0) REVERT: E 375 LYS cc_start: 0.8319 (tttt) cc_final: 0.8080 (tptp) REVERT: I 351 GLN cc_start: 0.7697 (tt0) cc_final: 0.7288 (tm-30) REVERT: J 308 ILE cc_start: 0.8608 (pt) cc_final: 0.8274 (mp) outliers start: 6 outliers final: 6 residues processed: 65 average time/residue: 0.4034 time to fit residues: 34.4309 Evaluate side-chains 55 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain J residue 346 PHE Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS B 362 HIS C 329 HIS F 362 HIS G 329 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.082429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.071013 restraints weight = 77509.458| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 6.40 r_work: 0.4004 rms_B_bonded: 5.82 restraints_weight: 2.0000 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5830 Z= 0.267 Angle : 0.686 6.076 7800 Z= 0.369 Chirality : 0.050 0.144 880 Planarity : 0.004 0.027 990 Dihedral : 5.913 18.246 770 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 2.42 % Allowed : 11.52 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.16 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 374 PHE 0.011 0.002 PHE E 378 TYR 0.007 0.002 TYR C 310 ARG 0.004 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 160) hydrogen bonds : angle 6.02279 ( 480) covalent geometry : bond 0.00555 ( 5830) covalent geometry : angle 0.68557 ( 7800) *********************** 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 52 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 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 375 LYS cc_start: 0.9131 (tttt) cc_final: 0.8921 (tttp) REVERT: B 378 PHE cc_start: 0.8476 (t80) cc_final: 0.8131 (t80) REVERT: D 372 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8575 (mp0) REVERT: E 375 LYS cc_start: 0.8441 (tttt) cc_final: 0.8128 (tptp) REVERT: I 351 GLN cc_start: 0.7753 (tt0) cc_final: 0.7303 (tm-30) REVERT: J 308 ILE cc_start: 0.8632 (pt) cc_final: 0.8289 (mp) outliers start: 16 outliers final: 12 residues processed: 46 average time/residue: 0.5740 time to fit residues: 34.6017 Evaluate side-chains 48 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 346 PHE 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 G residue 371 ILE Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain J residue 346 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 13 optimal weight: 0.0670 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.083259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.071730 restraints weight = 76692.631| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 6.38 r_work: 0.4028 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5830 Z= 0.145 Angle : 0.560 5.313 7800 Z= 0.297 Chirality : 0.050 0.130 880 Planarity : 0.003 0.029 990 Dihedral : 5.337 17.273 770 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.52 % Allowed : 11.97 % Favored : 86.52 % 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: -3.15 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 362 PHE 0.007 0.001 PHE F 346 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 160) hydrogen bonds : angle 5.63410 ( 480) covalent geometry : bond 0.00296 ( 5830) covalent geometry : angle 0.55996 ( 7800) *********************** 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 53 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 2.645 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: B 378 PHE cc_start: 0.8679 (t80) cc_final: 0.8260 (t80) REVERT: D 372 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8568 (mp0) REVERT: E 375 LYS cc_start: 0.8467 (tttt) cc_final: 0.8138 (tptp) REVERT: F 346 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8078 (p90) REVERT: G 340 LYS cc_start: 0.7586 (mttt) cc_final: 0.7259 (tptp) REVERT: I 351 GLN cc_start: 0.7804 (tt0) cc_final: 0.7412 (tm-30) REVERT: J 308 ILE cc_start: 0.8644 (pt) cc_final: 0.8318 (mp) outliers start: 10 outliers final: 9 residues processed: 49 average time/residue: 0.5649 time to fit residues: 37.1196 Evaluate side-chains 50 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 357 LEU 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 J residue 346 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.081402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.070106 restraints weight = 80157.897| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 6.32 r_work: 0.3986 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.7398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5830 Z= 0.260 Angle : 0.654 6.107 7800 Z= 0.351 Chirality : 0.050 0.146 880 Planarity : 0.004 0.031 990 Dihedral : 5.886 17.674 770 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 2.88 % Allowed : 11.97 % Favored : 85.15 % 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: -3.39 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 330 PHE 0.009 0.002 PHE F 346 TYR 0.007 0.002 TYR B 310 ARG 0.004 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.05002 ( 160) hydrogen bonds : angle 5.75295 ( 480) covalent geometry : bond 0.00544 ( 5830) covalent geometry : angle 0.65397 ( 7800) *********************** 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 54 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8619 (mttt) cc_final: 0.8069 (pptt) REVERT: B 378 PHE cc_start: 0.8679 (t80) cc_final: 0.8349 (t80) REVERT: D 372 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8561 (mp0) REVERT: F 346 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7982 (p90) REVERT: I 351 GLN cc_start: 0.7741 (tt0) cc_final: 0.7249 (tm-30) outliers start: 19 outliers final: 15 residues processed: 49 average time/residue: 0.4316 time to fit residues: 28.8872 Evaluate side-chains 47 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 357 LEU 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 308 ILE Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 348 ASP Chi-restraints excluded: chain I residue 357 LEU 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 32 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 61 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.082309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.070979 restraints weight = 77685.548| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 6.25 r_work: 0.3999 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.158 Angle : 0.563 5.397 7800 Z= 0.299 Chirality : 0.049 0.133 880 Planarity : 0.003 0.033 990 Dihedral : 5.385 15.813 770 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.52 % Allowed : 13.33 % Favored : 85.15 % 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: -3.38 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 362 PHE 0.007 0.001 PHE A 378 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 160) hydrogen bonds : angle 5.47198 ( 480) covalent geometry : bond 0.00323 ( 5830) covalent geometry : angle 0.56313 ( 7800) *********************** 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 45 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 378 PHE cc_start: 0.8696 (t80) cc_final: 0.8383 (t80) REVERT: D 372 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8530 (mp0) REVERT: F 346 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7975 (p90) REVERT: I 351 GLN cc_start: 0.7711 (tt0) cc_final: 0.7332 (tm-30) outliers start: 10 outliers final: 9 residues processed: 43 average time/residue: 0.4197 time to fit residues: 25.8407 Evaluate side-chains 43 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 357 LEU 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 J residue 346 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.081621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.070415 restraints weight = 79342.679| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 6.25 r_work: 0.3990 rms_B_bonded: 5.81 restraints_weight: 2.0000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.7741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5830 Z= 0.221 Angle : 0.609 5.846 7800 Z= 0.326 Chirality : 0.049 0.142 880 Planarity : 0.004 0.033 990 Dihedral : 5.631 15.730 770 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.12 % Allowed : 13.03 % 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: -3.56 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.008 0.002 PHE F 346 TYR 0.009 0.002 TYR B 310 ARG 0.003 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 160) hydrogen bonds : angle 5.53247 ( 480) covalent geometry : bond 0.00459 ( 5830) covalent geometry : angle 0.60902 ( 7800) *********************** 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 46 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 378 PHE cc_start: 0.8644 (t80) cc_final: 0.8253 (t80) REVERT: D 372 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8496 (mp0) REVERT: F 346 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7936 (p90) REVERT: I 351 GLN cc_start: 0.7657 (tt0) cc_final: 0.7284 (tm-30) outliers start: 14 outliers final: 13 residues processed: 41 average time/residue: 0.3827 time to fit residues: 21.8696 Evaluate side-chains 45 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain C residue 357 LEU 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 357 LEU 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 28 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.082597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.071396 restraints weight = 77735.754| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 6.20 r_work: 0.4029 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.7837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5830 Z= 0.172 Angle : 0.565 5.414 7800 Z= 0.301 Chirality : 0.049 0.133 880 Planarity : 0.003 0.034 990 Dihedral : 5.351 14.511 770 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.36 % Allowed : 13.64 % Favored : 85.00 % 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: -3.59 (0.23), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 362 PHE 0.011 0.002 PHE A 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 160) hydrogen bonds : angle 5.37685 ( 480) covalent geometry : bond 0.00358 ( 5830) covalent geometry : angle 0.56521 ( 7800) ********************** 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 40 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 378 PHE cc_start: 0.8580 (t80) cc_final: 0.8212 (t80) REVERT: D 372 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8591 (mp0) REVERT: F 346 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8119 (p90) outliers start: 9 outliers final: 7 residues processed: 38 average time/residue: 0.3784 time to fit residues: 20.0650 Evaluate side-chains 37 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 357 LEU 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 G residue 358 ASP Chi-restraints excluded: chain H residue 346 PHE 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 27 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 20 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.082733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.071544 restraints weight = 77649.298| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 6.13 r_work: 0.4024 rms_B_bonded: 5.63 restraints_weight: 2.0000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.7959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5830 Z= 0.146 Angle : 0.545 5.355 7800 Z= 0.290 Chirality : 0.050 0.133 880 Planarity : 0.003 0.033 990 Dihedral : 5.179 14.389 770 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.21 % Allowed : 13.94 % 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: -3.56 (0.24), residues: 730 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.011 0.001 PHE A 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 160) hydrogen bonds : angle 5.28613 ( 480) covalent geometry : bond 0.00305 ( 5830) covalent geometry : angle 0.54546 ( 7800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6177.51 seconds wall clock time: 109 minutes 33.06 seconds (6573.06 seconds total)