Starting phenix.real_space_refine on Thu Sep 10 20:33:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wtw_66225/09_2026/9wtw_66225.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wtw_66225/09_2026/9wtw_66225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wtw_66225/09_2026/9wtw_66225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wtw_66225/09_2026/9wtw_66225.map" model { file = "/net/cci-nas-00/data/ceres_data/9wtw_66225/09_2026/9wtw_66225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wtw_66225/09_2026/9wtw_66225.cif" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1930 2.51 5 N 530 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3090 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Restraints were copied for chains: J, I, H, G, A, D, C, F, E Time building chain proxies: 0.59, per 1000 atoms: 0.19 Number of scatterers: 3090 At special positions: 0 Unit cell: (77.4117, 65.9433, 45.8736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 620 8.00 N 530 7.00 C 1930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 115.6 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 67.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 2 through 6 removed outlier: 6.335A pdb=" N GLU J 3 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N HIS H 6 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG J 5 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU B 3 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N HIS D 6 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 5 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU D 3 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N HIS F 6 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG D 5 " --> pdb=" O HIS F 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 10 through 20 removed outlier: 6.991A pdb=" N GLU J 11 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL H 12 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS J 13 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS H 14 " --> pdb=" O HIS J 13 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N TYR B 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N HIS H 13 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL B 12 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N GLN H 15 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N HIS B 14 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU H 17 " --> pdb=" O HIS B 14 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS B 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N PHE H 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU B 11 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL D 12 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS B 13 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS D 14 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU D 11 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL F 12 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS D 13 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS F 14 " --> pdb=" O HIS D 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 23 through 25 removed outlier: 6.682A pdb=" N ASP B 23 " --> pdb=" O VAL H 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 28 through 39 removed outlier: 6.805A pdb=" N GLY J 29 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE H 32 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE J 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU H 34 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY J 33 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N VAL H 36 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET J 35 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N GLY H 38 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLY J 37 " --> pdb=" O GLY H 38 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET H 35 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 36 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY H 37 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY B 38 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL H 39 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY B 29 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE D 32 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU D 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY B 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N VAL D 36 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET B 35 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N GLY D 38 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLY B 37 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY D 29 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE F 32 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU F 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY D 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N VAL F 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET D 35 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N GLY F 38 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLY D 37 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 2 through 6 removed outlier: 6.335A pdb=" N GLU I 3 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N HIS G 6 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG I 5 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU G 3 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N HIS A 6 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG G 5 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A 3 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N HIS C 6 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 5 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU C 3 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N HIS E 6 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG C 5 " --> pdb=" O HIS E 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 20 removed outlier: 6.991A pdb=" N GLU I 11 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL G 12 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS I 13 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS G 14 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU G 11 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 12 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS G 13 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS A 14 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU A 11 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 12 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS A 13 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS C 14 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU C 11 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL E 12 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS C 13 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS E 14 " --> pdb=" O HIS C 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 23 through 25 Processing sheet with id=AA8, first strand: chain 'I' and resid 28 through 39 removed outlier: 6.804A pdb=" N GLY I 29 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE G 32 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE I 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU G 34 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY I 33 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N VAL G 36 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET I 35 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N GLY G 38 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLY I 37 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY G 29 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE A 32 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE G 31 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU A 34 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY G 33 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N VAL A 36 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET G 35 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N GLY A 38 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLY G 37 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY A 29 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ILE C 32 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N VAL C 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET A 35 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N GLY C 38 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLY A 37 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY C 29 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE E 32 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE C 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU E 34 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY C 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N VAL E 36 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N MET C 35 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N GLY E 38 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N GLY C 37 " --> pdb=" O GLY E 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 65 hydrogen bonds defined for protein. 195 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: 0.33 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 862 1.33 - 1.45: 548 1.45 - 1.57: 1680 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3110 Sorted by residual: bond pdb=" ND1 HIS I 13 " pdb=" CE1 HIS I 13 " ideal model delta sigma weight residual 1.321 1.348 -0.027 1.00e-02 1.00e+04 7.37e+00 bond pdb=" ND1 HIS J 13 " pdb=" CE1 HIS J 13 " ideal model delta sigma weight residual 1.321 1.348 -0.027 1.00e-02 1.00e+04 7.37e+00 bond pdb=" ND1 HIS E 13 " pdb=" CE1 HIS E 13 " ideal model delta sigma weight residual 1.321 1.348 -0.027 1.00e-02 1.00e+04 7.22e+00 bond pdb=" ND1 HIS H 13 " pdb=" CE1 HIS H 13 " ideal model delta sigma weight residual 1.321 1.348 -0.027 1.00e-02 1.00e+04 7.21e+00 bond pdb=" ND1 HIS F 13 " pdb=" CE1 HIS F 13 " ideal model delta sigma weight residual 1.321 1.348 -0.027 1.00e-02 1.00e+04 7.17e+00 ... (remaining 3105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 2396 1.45 - 2.89: 1284 2.89 - 4.34: 370 4.34 - 5.78: 97 5.78 - 7.23: 23 Bond angle restraints: 4170 Sorted by residual: angle pdb=" CB HIS I 14 " pdb=" CG HIS I 14 " pdb=" CD2 HIS I 14 " ideal model delta sigma weight residual 131.20 124.79 6.41 1.30e+00 5.92e-01 2.43e+01 angle pdb=" CB HIS J 14 " pdb=" CG HIS J 14 " pdb=" CD2 HIS J 14 " ideal model delta sigma weight residual 131.20 124.81 6.39 1.30e+00 5.92e-01 2.42e+01 angle pdb=" CB HIS F 14 " pdb=" CG HIS F 14 " pdb=" CD2 HIS F 14 " ideal model delta sigma weight residual 131.20 124.84 6.36 1.30e+00 5.92e-01 2.40e+01 angle pdb=" CB HIS C 14 " pdb=" CG HIS C 14 " pdb=" CD2 HIS C 14 " ideal model delta sigma weight residual 131.20 124.84 6.36 1.30e+00 5.92e-01 2.39e+01 angle pdb=" CB HIS D 14 " pdb=" CG HIS D 14 " pdb=" CD2 HIS D 14 " ideal model delta sigma weight residual 131.20 124.84 6.36 1.30e+00 5.92e-01 2.39e+01 ... (remaining 4165 not shown) Histogram of dihedral angle deviations from ideal: 0.08 - 13.45: 1557 13.45 - 26.82: 83 26.82 - 40.19: 50 40.19 - 53.57: 30 53.57 - 66.94: 10 Dihedral angle restraints: 1730 sinusoidal: 670 harmonic: 1060 Sorted by residual: dihedral pdb=" CA VAL D 39 " pdb=" C VAL D 39 " pdb=" N VAL D 40 " pdb=" CA VAL D 40 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA VAL J 39 " pdb=" C VAL J 39 " pdb=" N VAL J 40 " pdb=" CA VAL J 40 " ideal model delta harmonic sigma weight residual -180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA VAL I 39 " pdb=" C VAL I 39 " pdb=" N VAL I 40 " pdb=" CA VAL I 40 " ideal model delta harmonic sigma weight residual -180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 1727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 144 0.056 - 0.111: 188 0.111 - 0.166: 48 0.166 - 0.221: 20 0.221 - 0.277: 30 Chirality restraints: 430 Sorted by residual: chirality pdb=" CA HIS F 13 " pdb=" N HIS F 13 " pdb=" C HIS F 13 " pdb=" CB HIS F 13 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA HIS G 13 " pdb=" N HIS G 13 " pdb=" C HIS G 13 " pdb=" CB HIS G 13 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA HIS D 13 " pdb=" N HIS D 13 " pdb=" C HIS D 13 " pdb=" CB HIS D 13 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 427 not shown) Planarity restraints: 560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 10 " -0.110 2.00e-02 2.50e+03 6.49e-02 8.43e+01 pdb=" CG TYR H 10 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR H 10 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR H 10 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR H 10 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR H 10 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR H 10 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR H 10 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 10 " 0.110 2.00e-02 2.50e+03 6.49e-02 8.43e+01 pdb=" CG TYR E 10 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 10 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR E 10 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR E 10 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR E 10 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR E 10 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 10 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 10 " 0.110 2.00e-02 2.50e+03 6.49e-02 8.43e+01 pdb=" CG TYR G 10 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR G 10 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR G 10 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR G 10 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR G 10 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR G 10 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 10 " 0.109 2.00e-02 2.50e+03 ... (remaining 557 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 521 2.83 - 3.35: 2378 3.35 - 3.86: 5029 3.86 - 4.38: 5653 4.38 - 4.90: 9529 Nonbonded interactions: 23110 Sorted by model distance: nonbonded pdb=" OG SER G 26 " pdb=" OD2 ASP F 1 " model vdw 2.312 3.040 nonbonded pdb=" OG SER H 26 " pdb=" OD2 ASP E 1 " model vdw 2.312 3.040 nonbonded pdb=" OG SER I 26 " pdb=" OD2 ASP D 1 " model vdw 2.312 3.040 nonbonded pdb=" OG SER J 26 " pdb=" OD2 ASP C 1 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASP C 23 " pdb=" O HOH C 101 " model vdw 2.442 3.040 ... (remaining 23105 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 'B' selection = chain 'J' selection = chain 'I' selection = chain 'H' selection = chain 'G' selection = chain 'A' selection = chain 'D' selection = chain 'C' selection = chain 'F' selection = chain 'E' } 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: 2.870 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 : 0.013 0.034 3110 Z= 0.855 Angle : 1.887 7.226 4170 Z= 1.278 Chirality : 0.102 0.277 430 Planarity : 0.016 0.079 560 Dihedral : 14.101 66.939 1070 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.23 % Allowed : 3.23 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.37), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.002 ARG H 5 TYR 0.110 0.055 TYR H 10 PHE 0.015 0.005 PHE D 20 HIS 0.004 0.002 HIS I 14 Details of bonding type rmsd/Z covalent geometry : bond 0.01321 / 0.86 ( 3110) covalent geometry : angle 1.88715 / 1.28 ( 4170) hydrogen bonds : bond 0.17097 / 11.82 ( 65) hydrogen bonds : angle 8.00552 / 5.68 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.122 Fit side-chains REVERT: B 22 GLU cc_start: 0.8316 (tp30) cc_final: 0.8085 (tt0) REVERT: J 22 GLU cc_start: 0.8472 (tp30) cc_final: 0.8249 (mp0) REVERT: I 22 GLU cc_start: 0.8470 (tp30) cc_final: 0.8248 (mp0) REVERT: H 22 GLU cc_start: 0.8426 (tp30) cc_final: 0.8155 (tt0) REVERT: G 22 GLU cc_start: 0.8427 (tp30) cc_final: 0.8157 (tt0) REVERT: A 22 GLU cc_start: 0.8315 (tp30) cc_final: 0.8084 (tt0) REVERT: D 22 GLU cc_start: 0.8328 (tp30) cc_final: 0.7987 (mp0) REVERT: C 22 GLU cc_start: 0.8312 (tp30) cc_final: 0.7972 (mp0) REVERT: F 22 GLU cc_start: 0.8528 (tp30) cc_final: 0.8254 (mp0) REVERT: E 22 GLU cc_start: 0.8527 (tp30) cc_final: 0.8254 (mp0) outliers start: 10 outliers final: 4 residues processed: 137 average time/residue: 0.5690 time to fit residues: 79.7395 Evaluate side-chains 130 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 HIS B 15 GLN J 15 GLN I 15 GLN H 15 GLN G 15 GLN A 6 HIS A 15 GLN D 15 GLN C 15 GLN F 6 HIS F 15 GLN E 15 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.148629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110640 restraints weight = 2300.226| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.59 r_work: 0.3446 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3110 Z= 0.149 Angle : 0.592 3.956 4170 Z= 0.349 Chirality : 0.060 0.147 430 Planarity : 0.002 0.010 560 Dihedral : 7.968 48.268 428 Min Nonbonded Distance : 2.693 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.23 % Allowed : 9.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.36), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 5 TYR 0.008 0.002 TYR E 10 PHE 0.012 0.002 PHE C 19 HIS 0.005 0.002 HIS E 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 ( 3110) covalent geometry : angle 0.59247 / 0.35 ( 4170) hydrogen bonds : bond 0.04193 / 2.90 ( 65) hydrogen bonds : angle 5.90342 / 4.21 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.122 Fit side-chains REVERT: B 5 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8069 (mtp85) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 0.6191 time to fit residues: 78.4477 Evaluate side-chains 125 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.143271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.105134 restraints weight = 2267.367| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.57 r_work: 0.3366 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3110 Z= 0.240 Angle : 0.804 6.889 4170 Z= 0.448 Chirality : 0.066 0.166 430 Planarity : 0.003 0.013 560 Dihedral : 6.965 45.406 424 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.84 % Allowed : 9.03 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.35), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 5 TYR 0.010 0.004 TYR H 10 PHE 0.018 0.003 PHE C 19 HIS 0.011 0.003 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.24 ( 3110) covalent geometry : angle 0.80372 / 0.45 ( 4170) hydrogen bonds : bond 0.06431 / 4.50 ( 65) hydrogen bonds : angle 6.75777 / 4.79 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.134 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 130 average time/residue: 0.6298 time to fit residues: 83.5874 Evaluate side-chains 134 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 6 HIS I 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.145184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.107430 restraints weight = 2309.020| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.58 r_work: 0.3407 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3110 Z= 0.160 Angle : 0.629 5.285 4170 Z= 0.358 Chirality : 0.061 0.156 430 Planarity : 0.002 0.008 560 Dihedral : 6.742 47.154 424 Min Nonbonded Distance : 2.695 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.19 % Allowed : 10.32 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.35), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 5 TYR 0.008 0.003 TYR G 10 PHE 0.013 0.002 PHE C 19 HIS 0.007 0.002 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 3110) covalent geometry : angle 0.62900 / 0.36 ( 4170) hydrogen bonds : bond 0.05091 / 3.54 ( 65) hydrogen bonds : angle 6.34725 / 4.48 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.123 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 127 average time/residue: 0.6131 time to fit residues: 79.4474 Evaluate side-chains 134 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 6 HIS I 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.142710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105066 restraints weight = 2283.014| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.56 r_work: 0.3362 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3110 Z= 0.263 Angle : 0.837 7.642 4170 Z= 0.466 Chirality : 0.067 0.170 430 Planarity : 0.003 0.011 560 Dihedral : 6.902 48.230 424 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.52 % Allowed : 9.68 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 5 TYR 0.009 0.004 TYR E 10 PHE 0.021 0.003 PHE D 19 HIS 0.011 0.003 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.26 ( 3110) covalent geometry : angle 0.83737 / 0.47 ( 4170) hydrogen bonds : bond 0.07015 / 4.89 ( 65) hydrogen bonds : angle 6.81756 / 4.92 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.087 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 0.6069 time to fit residues: 79.8976 Evaluate side-chains 134 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 6 HIS I 6 HIS H 6 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.142727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.105124 restraints weight = 2286.583| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.57 r_work: 0.3365 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3110 Z= 0.251 Angle : 0.850 11.109 4170 Z= 0.461 Chirality : 0.067 0.166 430 Planarity : 0.003 0.014 560 Dihedral : 6.898 48.082 424 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.87 % Allowed : 10.32 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG H 5 TYR 0.009 0.004 TYR D 10 PHE 0.021 0.003 PHE C 19 HIS 0.009 0.003 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 ( 3110) covalent geometry : angle 0.85023 / 0.46 ( 4170) hydrogen bonds : bond 0.06671 / 4.65 ( 65) hydrogen bonds : angle 6.53921 / 4.74 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.130 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.6160 time to fit residues: 81.7858 Evaluate side-chains 137 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 6 HIS H 6 HIS G 6 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.141964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.104428 restraints weight = 2340.967| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.59 r_work: 0.3355 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 3110 Z= 0.310 Angle : 0.954 12.499 4170 Z= 0.519 Chirality : 0.071 0.173 430 Planarity : 0.004 0.014 560 Dihedral : 7.003 49.314 424 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.87 % Allowed : 11.29 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 5 TYR 0.012 0.005 TYR J 10 PHE 0.025 0.003 PHE D 19 HIS 0.010 0.003 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.31 ( 3110) covalent geometry : angle 0.95387 / 0.52 ( 4170) hydrogen bonds : bond 0.07753 / 5.42 ( 65) hydrogen bonds : angle 6.60912 / 4.81 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.125 Fit side-chains REVERT: D 22 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7948 (tt0) REVERT: C 22 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8044 (tt0) outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.6088 time to fit residues: 80.1381 Evaluate side-chains 136 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 HIS G 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.144161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.106761 restraints weight = 2364.130| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.58 r_work: 0.3392 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3110 Z= 0.173 Angle : 0.692 7.892 4170 Z= 0.382 Chirality : 0.062 0.154 430 Planarity : 0.002 0.008 560 Dihedral : 6.853 48.247 424 Min Nonbonded Distance : 2.683 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.58 % Allowed : 12.90 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 5 TYR 0.010 0.003 TYR H 10 PHE 0.017 0.002 PHE C 19 HIS 0.007 0.002 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 ( 3110) covalent geometry : angle 0.69224 / 0.38 ( 4170) hydrogen bonds : bond 0.05436 / 3.77 ( 65) hydrogen bonds : angle 6.02830 / 4.33 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.129 Fit side-chains REVERT: D 22 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7823 (mm-30) outliers start: 8 outliers final: 8 residues processed: 126 average time/residue: 0.6294 time to fit residues: 80.9906 Evaluate side-chains 134 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 HIS G 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104736 restraints weight = 2341.357| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.58 r_work: 0.3358 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 3110 Z= 0.310 Angle : 0.956 12.015 4170 Z= 0.521 Chirality : 0.071 0.173 430 Planarity : 0.004 0.012 560 Dihedral : 7.008 49.632 424 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.19 % Allowed : 11.61 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG J 5 TYR 0.014 0.005 TYR H 10 PHE 0.024 0.003 PHE D 19 HIS 0.009 0.003 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.31 ( 3110) covalent geometry : angle 0.95626 / 0.52 ( 4170) hydrogen bonds : bond 0.07778 / 5.42 ( 65) hydrogen bonds : angle 6.55755 / 4.77 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.122 Fit side-chains REVERT: D 22 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7969 (tt0) outliers start: 13 outliers final: 9 residues processed: 128 average time/residue: 0.6366 time to fit residues: 83.2292 Evaluate side-chains 137 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 HIS G 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.143531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.106400 restraints weight = 2264.209| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.55 r_work: 0.3388 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3110 Z= 0.197 Angle : 0.751 9.422 4170 Z= 0.411 Chirality : 0.064 0.155 430 Planarity : 0.003 0.008 560 Dihedral : 6.897 47.703 424 Min Nonbonded Distance : 2.681 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.90 % Allowed : 13.55 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 5 TYR 0.011 0.004 TYR C 10 PHE 0.018 0.002 PHE C 19 HIS 0.007 0.003 HIS C 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 ( 3110) covalent geometry : angle 0.75144 / 0.41 ( 4170) hydrogen bonds : bond 0.05851 / 4.06 ( 65) hydrogen bonds : angle 6.09549 / 4.37 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.132 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 127 average time/residue: 0.6375 time to fit residues: 82.6522 Evaluate side-chains 136 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain A residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 HIS G 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.141943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104619 restraints weight = 2317.147| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.57 r_work: 0.3369 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 3110 Z= 0.275 Angle : 0.915 12.429 4170 Z= 0.492 Chirality : 0.069 0.170 430 Planarity : 0.003 0.010 560 Dihedral : 6.984 49.110 424 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.90 % Allowed : 14.19 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.34), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 5 TYR 0.013 0.005 TYR H 10 PHE 0.022 0.003 PHE C 19 HIS 0.009 0.003 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.28 ( 3110) covalent geometry : angle 0.91508 / 0.49 ( 4170) hydrogen bonds : bond 0.07252 / 5.07 ( 65) hydrogen bonds : angle 6.39870 / 4.64 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.15 seconds wall clock time: 34 minutes 59.08 seconds (2099.08 seconds total)