Starting phenix.real_space_refine on Tue Mar 3 12:20:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6osj_20183/03_2026/6osj_20183.cif Found real_map, /net/cci-nas-00/data/ceres_data/6osj_20183/03_2026/6osj_20183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6osj_20183/03_2026/6osj_20183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6osj_20183/03_2026/6osj_20183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6osj_20183/03_2026/6osj_20183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6osj_20183/03_2026/6osj_20183.map" } resolution = 2.8 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= 0.009 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: 3 Type Number sf(0) Gaussians C 2650 2.51 5 N 730 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4210 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.45, per 1000 atoms: 0.11 Number of scatterers: 4210 At special positions: 0 Unit cell: (92.22, 75.26, 40.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 830 8.00 N 730 7.00 C 2650 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: 0.37 Conformation dependent library (CDL) restraints added in 148.9 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.687A pdb=" N GLU A 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N VAL C 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS C 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL E 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY C 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS E 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL G 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLY E 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS G 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL I 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY G 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 58 removed outlier: 6.572A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ALA E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LYS E 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU C 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ALA G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL E 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS G 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU E 57 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ALA I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS I 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU G 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 82 removed outlier: 6.828A pdb=" N VAL A 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY C 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN C 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS A 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL C 70 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL E 71 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C 72 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY E 73 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA C 78 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN E 79 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS C 80 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 82 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL E 70 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL G 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR E 72 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY G 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA E 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN G 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS E 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR G 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL E 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL G 70 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL I 71 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR G 72 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY I 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL I 77 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA G 78 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN I 79 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS G 80 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR I 81 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 82 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 90 removed outlier: 6.490A pdb=" N ALA A 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA E 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA G 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.625A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS F 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL H 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY F 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 58 removed outlier: 6.627A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LYS D 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ALA F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LYS F 58 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU D 57 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS H 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU F 57 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 69 through 82 removed outlier: 6.935A pdb=" N VAL B 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY D 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL D 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA B 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN D 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS B 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR D 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL D 70 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR D 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY F 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL F 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN F 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS D 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR F 81 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL D 82 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL F 70 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL H 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR F 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY H 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL H 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA F 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN H 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS F 80 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR H 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL F 82 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL H 70 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL J 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR H 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY J 73 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL J 77 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA H 78 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN J 79 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS H 80 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR J 81 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL H 82 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 90 removed outlier: 6.464A pdb=" N ALA B 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA D 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA F 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA H 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 29 hydrogen bonds defined for protein. 87 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: 0.60 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 720 1.29 - 1.35: 660 1.35 - 1.42: 170 1.42 - 1.48: 781 1.48 - 1.55: 1899 Bond restraints: 4230 Sorted by residual: bond pdb=" CA ALA F 89 " pdb=" CB ALA F 89 " ideal model delta sigma weight residual 1.531 1.466 0.065 3.12e-02 1.03e+03 4.33e+00 bond pdb=" CA ALA C 89 " pdb=" CB ALA C 89 " ideal model delta sigma weight residual 1.531 1.466 0.065 3.12e-02 1.03e+03 4.29e+00 bond pdb=" CA ALA D 89 " pdb=" CB ALA D 89 " ideal model delta sigma weight residual 1.531 1.466 0.065 3.12e-02 1.03e+03 4.29e+00 bond pdb=" CA ALA I 89 " pdb=" CB ALA I 89 " ideal model delta sigma weight residual 1.531 1.466 0.064 3.12e-02 1.03e+03 4.27e+00 bond pdb=" CA ALA B 89 " pdb=" CB ALA B 89 " ideal model delta sigma weight residual 1.531 1.466 0.064 3.12e-02 1.03e+03 4.23e+00 ... (remaining 4225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 5344 1.77 - 3.54: 296 3.54 - 5.30: 46 5.30 - 7.07: 14 7.07 - 8.84: 20 Bond angle restraints: 5720 Sorted by residual: angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.41 112.57 8.84 1.83e+00 2.99e-01 2.33e+01 angle pdb=" C VAL H 49 " pdb=" N HIS H 50 " pdb=" CA HIS H 50 " ideal model delta sigma weight residual 121.41 112.58 8.83 1.83e+00 2.99e-01 2.33e+01 angle pdb=" C VAL J 49 " pdb=" N HIS J 50 " pdb=" CA HIS J 50 " ideal model delta sigma weight residual 121.41 112.58 8.83 1.83e+00 2.99e-01 2.33e+01 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 121.41 112.59 8.82 1.83e+00 2.99e-01 2.32e+01 angle pdb=" C VAL F 49 " pdb=" N HIS F 50 " pdb=" CA HIS F 50 " ideal model delta sigma weight residual 121.41 112.59 8.82 1.83e+00 2.99e-01 2.32e+01 ... (remaining 5715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.29: 2170 13.29 - 26.57: 220 26.57 - 39.85: 40 39.85 - 53.14: 20 53.14 - 66.42: 20 Dihedral angle restraints: 2470 sinusoidal: 820 harmonic: 1650 Sorted by residual: dihedral pdb=" CA GLY F 51 " pdb=" C GLY F 51 " pdb=" N VAL F 52 " pdb=" CA VAL F 52 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA GLY H 51 " pdb=" C GLY H 51 " pdb=" N VAL H 52 " pdb=" CA VAL H 52 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLY C 51 " pdb=" C GLY C 51 " pdb=" N VAL C 52 " pdb=" CA VAL C 52 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 533 0.064 - 0.128: 187 0.128 - 0.192: 20 0.192 - 0.256: 10 0.256 - 0.320: 10 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA HIS A 50 " pdb=" N HIS A 50 " pdb=" C HIS A 50 " pdb=" CB HIS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA HIS I 50 " pdb=" N HIS I 50 " pdb=" C HIS I 50 " pdb=" CB HIS I 50 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA HIS G 50 " pdb=" N HIS G 50 " pdb=" C HIS G 50 " pdb=" CB HIS G 50 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 757 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " 0.020 2.00e-02 2.50e+03 1.09e-02 2.37e+00 pdb=" CG TYR A 39 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 39 " 0.020 2.00e-02 2.50e+03 1.08e-02 2.35e+00 pdb=" CG TYR F 39 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR F 39 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR F 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 39 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 39 " 0.019 2.00e-02 2.50e+03 1.07e-02 2.29e+00 pdb=" CG TYR E 39 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR E 39 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR E 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 39 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 39 " 0.006 2.00e-02 2.50e+03 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 712 2.76 - 3.30: 3943 3.30 - 3.83: 6750 3.83 - 4.37: 7647 4.37 - 4.90: 15935 Nonbonded interactions: 34987 Sorted by model distance: nonbonded pdb=" OE2 GLU F 57 " pdb=" ND1 HIS G 50 " model vdw 2.227 3.120 nonbonded pdb=" OE2 GLU D 57 " pdb=" ND1 HIS E 50 " model vdw 2.258 3.120 nonbonded pdb=" OE2 GLU H 57 " pdb=" ND1 HIS I 50 " model vdw 2.260 3.120 nonbonded pdb=" OE2 GLU B 57 " pdb=" ND1 HIS C 50 " model vdw 2.264 3.120 nonbonded pdb=" O SER A 42 " pdb=" OG1 THR A 44 " model vdw 2.329 3.040 ... (remaining 34982 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: 0.730 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.030 Find NCS groups from input model: 0.020 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:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.011 0.065 4230 Z= 0.502 Angle : 1.127 8.838 5720 Z= 0.666 Chirality : 0.072 0.320 760 Planarity : 0.004 0.012 700 Dihedral : 13.688 66.424 1430 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % Rotamer: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % 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: -4.71 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.007 TYR A 39 PHE 0.010 0.003 PHE D 94 HIS 0.012 0.008 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.01111 ( 4230) covalent geometry : angle 1.12711 ( 5720) hydrogen bonds : bond 0.15412 ( 29) hydrogen bonds : angle 8.61744 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.177 Fit side-chains REVERT: D 83 GLU cc_start: 0.7176 (tt0) cc_final: 0.6916 (mt-10) REVERT: F 60 LYS cc_start: 0.7751 (mttt) cc_final: 0.7485 (ttmm) REVERT: F 65 ASN cc_start: 0.8171 (t0) cc_final: 0.7954 (t0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.5702 time to fit residues: 29.5366 Evaluate side-chains 37 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.217538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.194390 restraints weight = 4481.244| |-----------------------------------------------------------------------------| r_work (start): 0.4539 rms_B_bonded: 1.84 r_work: 0.4487 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4385 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4230 Z= 0.169 Angle : 0.744 6.002 5720 Z= 0.428 Chirality : 0.059 0.257 760 Planarity : 0.003 0.013 700 Dihedral : 5.938 16.935 610 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 4.88 % Allowed : 15.12 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.29 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.004 TYR D 39 PHE 0.009 0.002 PHE F 94 HIS 0.009 0.005 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4230) covalent geometry : angle 0.74396 ( 5720) hydrogen bonds : bond 0.04011 ( 29) hydrogen bonds : angle 5.84772 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.141 Fit side-chains REVERT: C 97 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7118 (mttm) REVERT: D 54 THR cc_start: 0.8719 (p) cc_final: 0.8245 (m) REVERT: G 38 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6561 (mm) REVERT: I 97 LYS cc_start: 0.7190 (mtpt) cc_final: 0.6981 (mttm) outliers start: 21 outliers final: 7 residues processed: 70 average time/residue: 0.3869 time to fit residues: 28.3714 Evaluate side-chains 46 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.193351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.170176 restraints weight = 4855.438| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 1.75 r_work: 0.4281 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4190 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 4230 Z= 0.397 Angle : 1.048 9.382 5720 Z= 0.607 Chirality : 0.070 0.342 760 Planarity : 0.004 0.015 700 Dihedral : 6.729 18.816 610 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.02 % Favored : 78.98 % Rotamer: Outliers : 8.14 % Allowed : 13.95 % Favored : 77.91 % 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: -4.28 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.007 TYR B 39 PHE 0.015 0.003 PHE A 94 HIS 0.013 0.007 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00849 ( 4230) covalent geometry : angle 1.04833 ( 5720) hydrogen bonds : bond 0.05150 ( 29) hydrogen bonds : angle 6.49590 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 46 time to evaluate : 0.128 Fit side-chains REVERT: A 60 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7598 (ttmt) REVERT: B 77 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8028 (m) REVERT: C 97 LYS cc_start: 0.7701 (mtpt) cc_final: 0.7306 (mttm) REVERT: D 54 THR cc_start: 0.8743 (p) cc_final: 0.8513 (p) REVERT: D 83 GLU cc_start: 0.7621 (tt0) cc_final: 0.7392 (mt-10) REVERT: G 65 ASN cc_start: 0.8105 (t0) cc_final: 0.7891 (t0) REVERT: J 83 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6873 (tt0) outliers start: 35 outliers final: 21 residues processed: 74 average time/residue: 0.3305 time to fit residues: 25.7172 Evaluate side-chains 67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.208340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.186852 restraints weight = 4652.498| |-----------------------------------------------------------------------------| r_work (start): 0.4521 rms_B_bonded: 1.92 r_work: 0.4454 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4357 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4230 Z= 0.137 Angle : 0.661 5.241 5720 Z= 0.379 Chirality : 0.057 0.238 760 Planarity : 0.002 0.011 700 Dihedral : 5.647 16.403 610 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 6.74 % Allowed : 17.91 % Favored : 75.35 % 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: -3.89 (0.31), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR A 39 PHE 0.019 0.003 PHE C 94 HIS 0.011 0.005 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4230) covalent geometry : angle 0.66134 ( 5720) hydrogen bonds : bond 0.03392 ( 29) hydrogen bonds : angle 5.27613 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 44 time to evaluate : 0.161 Fit side-chains REVERT: A 38 LEU cc_start: 0.4664 (OUTLIER) cc_final: 0.3525 (pp) REVERT: B 38 LEU cc_start: 0.4323 (OUTLIER) cc_final: 0.3519 (pp) REVERT: C 97 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7269 (mttm) REVERT: D 54 THR cc_start: 0.8544 (p) cc_final: 0.8234 (m) REVERT: F 54 THR cc_start: 0.8645 (p) cc_final: 0.8440 (m) REVERT: J 83 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6654 (tt0) outliers start: 29 outliers final: 13 residues processed: 65 average time/residue: 0.3379 time to fit residues: 23.0404 Evaluate side-chains 56 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.195739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.172869 restraints weight = 4855.844| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 1.77 r_work: 0.4324 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4230 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4230 Z= 0.328 Angle : 0.941 8.664 5720 Z= 0.546 Chirality : 0.066 0.313 760 Planarity : 0.004 0.014 700 Dihedral : 6.371 18.061 610 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.19 % Favored : 78.81 % Rotamer: Outliers : 8.14 % Allowed : 15.58 % Favored : 76.28 % 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: -3.95 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.006 TYR A 39 PHE 0.016 0.003 PHE C 94 HIS 0.012 0.007 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00695 ( 4230) covalent geometry : angle 0.94076 ( 5720) hydrogen bonds : bond 0.04782 ( 29) hydrogen bonds : angle 6.12585 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 0.111 Fit side-chains REVERT: A 38 LEU cc_start: 0.4405 (OUTLIER) cc_final: 0.3214 (pp) REVERT: B 38 LEU cc_start: 0.4477 (OUTLIER) cc_final: 0.3220 (pp) REVERT: C 97 LYS cc_start: 0.7688 (mtpt) cc_final: 0.7344 (mttm) REVERT: D 83 GLU cc_start: 0.7544 (tt0) cc_final: 0.7283 (mt-10) REVERT: E 46 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8484 (mt-10) REVERT: G 44 THR cc_start: 0.6732 (OUTLIER) cc_final: 0.6520 (m) REVERT: I 72 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8083 (p) REVERT: I 97 LYS cc_start: 0.7302 (mttm) cc_final: 0.7100 (mttm) REVERT: J 83 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6856 (tt0) outliers start: 35 outliers final: 23 residues processed: 69 average time/residue: 0.3158 time to fit residues: 23.0711 Evaluate side-chains 68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 10 optimal weight: 0.0050 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 56 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 overall best weight: 1.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.209636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.187538 restraints weight = 4799.014| |-----------------------------------------------------------------------------| r_work (start): 0.4533 rms_B_bonded: 1.77 r_work: 0.4468 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4369 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4230 Z= 0.134 Angle : 0.648 5.224 5720 Z= 0.372 Chirality : 0.057 0.232 760 Planarity : 0.002 0.011 700 Dihedral : 5.491 16.252 610 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 6.51 % Allowed : 18.37 % Favored : 75.12 % 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: -3.78 (0.31), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR A 39 PHE 0.011 0.002 PHE E 94 HIS 0.010 0.005 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4230) covalent geometry : angle 0.64850 ( 5720) hydrogen bonds : bond 0.03272 ( 29) hydrogen bonds : angle 5.31228 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 41 time to evaluate : 0.114 Fit side-chains REVERT: B 38 LEU cc_start: 0.4197 (OUTLIER) cc_final: 0.3533 (pp) REVERT: B 57 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: C 97 LYS cc_start: 0.7604 (mtpt) cc_final: 0.7264 (mttm) REVERT: I 72 THR cc_start: 0.8277 (p) cc_final: 0.8037 (p) REVERT: I 97 LYS cc_start: 0.7422 (mttm) cc_final: 0.7219 (mttm) REVERT: J 83 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6604 (tt0) outliers start: 28 outliers final: 22 residues processed: 64 average time/residue: 0.2988 time to fit residues: 20.2283 Evaluate side-chains 66 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 41 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.197219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.173374 restraints weight = 4721.641| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 1.86 r_work: 0.4316 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 4230 Z= 0.360 Angle : 0.983 9.051 5720 Z= 0.570 Chirality : 0.067 0.320 760 Planarity : 0.004 0.014 700 Dihedral : 6.422 18.364 610 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.02 % Favored : 78.98 % Rotamer: Outliers : 9.53 % Allowed : 15.81 % Favored : 74.65 % 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: -3.93 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.006 TYR C 39 PHE 0.013 0.003 PHE F 94 HIS 0.012 0.007 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00762 ( 4230) covalent geometry : angle 0.98282 ( 5720) hydrogen bonds : bond 0.04946 ( 29) hydrogen bonds : angle 6.19921 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 40 time to evaluate : 0.089 Fit side-chains REVERT: B 38 LEU cc_start: 0.4162 (OUTLIER) cc_final: 0.2978 (pp) REVERT: B 57 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: C 97 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7319 (mttm) REVERT: D 83 GLU cc_start: 0.7535 (tt0) cc_final: 0.7269 (mt-10) REVERT: I 72 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8018 (p) REVERT: I 97 LYS cc_start: 0.7210 (mttm) cc_final: 0.6989 (mttm) REVERT: J 83 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6990 (tt0) outliers start: 41 outliers final: 27 residues processed: 72 average time/residue: 0.2946 time to fit residues: 22.4203 Evaluate side-chains 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 40 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.203670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.179748 restraints weight = 4661.940| |-----------------------------------------------------------------------------| r_work (start): 0.4449 rms_B_bonded: 1.86 r_work: 0.4386 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4286 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4230 Z= 0.218 Angle : 0.792 7.455 5720 Z= 0.459 Chirality : 0.061 0.287 760 Planarity : 0.003 0.013 700 Dihedral : 5.955 18.330 610 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.59 % Favored : 84.41 % Rotamer: Outliers : 7.67 % Allowed : 17.67 % Favored : 74.65 % 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: -3.91 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR E 39 PHE 0.023 0.003 PHE C 94 HIS 0.012 0.006 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 4230) covalent geometry : angle 0.79171 ( 5720) hydrogen bonds : bond 0.04215 ( 29) hydrogen bonds : angle 5.69033 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 42 time to evaluate : 0.143 Fit side-chains REVERT: B 38 LEU cc_start: 0.4071 (OUTLIER) cc_final: 0.3033 (pp) REVERT: B 57 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: C 97 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7311 (mttm) REVERT: F 54 THR cc_start: 0.8669 (p) cc_final: 0.8435 (m) REVERT: G 80 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8206 (tttm) REVERT: H 38 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.4152 (tp) REVERT: I 72 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8003 (p) REVERT: J 83 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6821 (tt0) outliers start: 33 outliers final: 25 residues processed: 64 average time/residue: 0.3116 time to fit residues: 21.0935 Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 41 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 27 optimal weight: 0.3980 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 overall best weight: 4.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.203057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.179236 restraints weight = 4621.677| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 1.85 r_work: 0.4379 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4282 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4230 Z= 0.220 Angle : 0.801 7.504 5720 Z= 0.464 Chirality : 0.061 0.291 760 Planarity : 0.003 0.013 700 Dihedral : 5.914 18.040 610 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.47 % Favored : 81.53 % Rotamer: Outliers : 7.91 % Allowed : 18.14 % Favored : 73.95 % 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: -3.87 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.004 TYR E 39 PHE 0.013 0.003 PHE E 94 HIS 0.011 0.006 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 4230) covalent geometry : angle 0.80125 ( 5720) hydrogen bonds : bond 0.04403 ( 29) hydrogen bonds : angle 5.78619 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 39 time to evaluate : 0.181 Fit side-chains REVERT: A 38 LEU cc_start: 0.1110 (OUTLIER) cc_final: 0.0875 (pp) REVERT: B 38 LEU cc_start: 0.4107 (OUTLIER) cc_final: 0.3243 (pp) REVERT: B 57 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: C 97 LYS cc_start: 0.7714 (mtpt) cc_final: 0.7298 (mttm) REVERT: D 38 LEU cc_start: 0.4225 (OUTLIER) cc_final: 0.3914 (tm) REVERT: F 54 THR cc_start: 0.8654 (p) cc_final: 0.8400 (m) REVERT: G 38 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5305 (tp) REVERT: G 80 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8226 (tttm) REVERT: H 38 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.4131 (tp) REVERT: I 72 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7916 (p) REVERT: J 83 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6823 (tt0) outliers start: 34 outliers final: 22 residues processed: 62 average time/residue: 0.3010 time to fit residues: 19.8133 Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 39 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.203181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.179617 restraints weight = 4531.243| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 1.81 r_work: 0.4376 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4279 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4230 Z= 0.227 Angle : 0.804 7.632 5720 Z= 0.467 Chirality : 0.062 0.294 760 Planarity : 0.003 0.013 700 Dihedral : 5.937 17.963 610 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 7.91 % Allowed : 18.37 % Favored : 73.72 % 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: -3.86 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.004 TYR E 39 PHE 0.013 0.003 PHE E 94 HIS 0.012 0.006 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 4230) covalent geometry : angle 0.80445 ( 5720) hydrogen bonds : bond 0.04340 ( 29) hydrogen bonds : angle 5.74909 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 38 time to evaluate : 0.158 Fit side-chains REVERT: A 38 LEU cc_start: 0.1030 (OUTLIER) cc_final: 0.0786 (pp) REVERT: B 38 LEU cc_start: 0.4052 (OUTLIER) cc_final: 0.3194 (pp) REVERT: B 57 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: C 97 LYS cc_start: 0.7741 (mtpt) cc_final: 0.7343 (mttm) REVERT: D 38 LEU cc_start: 0.4177 (OUTLIER) cc_final: 0.3897 (tm) REVERT: F 54 THR cc_start: 0.8695 (p) cc_final: 0.8448 (m) REVERT: G 38 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5369 (tp) REVERT: G 80 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8243 (tttm) REVERT: H 38 LEU cc_start: 0.5556 (OUTLIER) cc_final: 0.4136 (tp) REVERT: I 72 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7902 (p) REVERT: J 83 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6840 (tt0) outliers start: 34 outliers final: 23 residues processed: 62 average time/residue: 0.2852 time to fit residues: 18.8515 Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.198544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.174527 restraints weight = 4677.822| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 1.86 r_work: 0.4333 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4236 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4230 Z= 0.319 Angle : 0.935 8.841 5720 Z= 0.544 Chirality : 0.066 0.324 760 Planarity : 0.004 0.014 700 Dihedral : 6.344 18.479 610 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.68 % Favored : 79.32 % Rotamer: Outliers : 7.21 % Allowed : 19.30 % Favored : 73.49 % 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: -3.96 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.005 TYR C 39 PHE 0.014 0.003 PHE E 94 HIS 0.012 0.007 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00677 ( 4230) covalent geometry : angle 0.93474 ( 5720) hydrogen bonds : bond 0.04947 ( 29) hydrogen bonds : angle 6.10281 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1318.08 seconds wall clock time: 23 minutes 20.41 seconds (1400.41 seconds total)