Starting phenix.real_space_refine on Wed Mar 5 23:46:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6osj_20183/03_2025/6osj_20183.cif Found real_map, /net/cci-nas-00/data/ceres_data/6osj_20183/03_2025/6osj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6osj_20183/03_2025/6osj_20183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6osj_20183/03_2025/6osj_20183.map" model { file = "/net/cci-nas-00/data/ceres_data/6osj_20183/03_2025/6osj_20183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6osj_20183/03_2025/6osj_20183.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.77, per 1000 atoms: 0.42 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: 0.91 Conformation dependent library (CDL) restraints added in 561.4 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: 0.46 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: 0.87 Time building geometry restraints manager: 1.09 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.010 Normalize map: mean=0, sd=1: 0.440 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.830 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- 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= 0.772 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.012 0.008 HIS B 50 PHE 0.010 0.003 PHE D 94 TYR 0.022 0.007 TYR A 39 *********************** 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 : 0.420 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: 1.1133 time to fit residues: 58.0140 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 : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4776 r_free = 0.4776 target = 0.220127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.197583 restraints weight = 4467.707| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 1.76 r_work: 0.4514 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4409 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1838 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= 0.214 Angle : 0.715 5.610 5720 Z= 0.410 Chirality : 0.058 0.242 760 Planarity : 0.002 0.013 700 Dihedral : 5.839 16.822 610 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 4.88 % Allowed : 13.72 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS F 50 PHE 0.008 0.002 PHE F 94 TYR 0.017 0.004 TYR D 39 *********************** 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 77 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.495 Fit side-chains REVERT: C 97 LYS cc_start: 0.7612 (mtpt) cc_final: 0.7192 (mttm) REVERT: D 54 THR cc_start: 0.8670 (p) cc_final: 0.8210 (m) REVERT: G 94 PHE cc_start: 0.8068 (p90) cc_final: 0.7849 (p90) REVERT: J 60 LYS cc_start: 0.8037 (mttt) cc_final: 0.7710 (ttmm) outliers start: 21 outliers final: 7 residues processed: 74 average time/residue: 1.0875 time to fit residues: 84.1059 Evaluate side-chains 49 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 H residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.4567 r_free = 0.4567 target = 0.193914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.170901 restraints weight = 4805.072| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.74 r_work: 0.4289 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 4230 Z= 0.567 Angle : 1.022 9.134 5720 Z= 0.592 Chirality : 0.069 0.331 760 Planarity : 0.004 0.015 700 Dihedral : 6.661 18.513 610 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.68 % Favored : 79.32 % Rotamer: Outliers : 7.44 % Allowed : 15.58 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS C 50 PHE 0.014 0.003 PHE A 94 TYR 0.019 0.006 TYR B 39 *********************** 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 76 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 44 time to evaluate : 0.428 Fit side-chains REVERT: B 38 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.4465 (pp) REVERT: B 77 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8045 (m) REVERT: C 97 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7300 (mttm) REVERT: D 54 THR cc_start: 0.8765 (p) cc_final: 0.8548 (p) REVERT: D 83 GLU cc_start: 0.7615 (tt0) cc_final: 0.7390 (mt-10) REVERT: J 83 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6875 (tt0) outliers start: 32 outliers final: 21 residues processed: 69 average time/residue: 0.7690 time to fit residues: 56.1088 Evaluate side-chains 63 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 39 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 92 THR Chi-restraints excluded: chain B residue 38 LEU 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 38 LEU Chi-restraints excluded: chain G residue 72 THR 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 1 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.4682 r_free = 0.4682 target = 0.204689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.182097 restraints weight = 4740.368| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 1.99 r_work: 0.4397 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4300 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4230 Z= 0.253 Angle : 0.742 6.607 5720 Z= 0.430 Chirality : 0.059 0.273 760 Planarity : 0.003 0.012 700 Dihedral : 5.869 16.918 610 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 7.21 % Allowed : 18.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.006 HIS C 50 PHE 0.019 0.003 PHE C 94 TYR 0.017 0.004 TYR A 39 *********************** 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: 31 poor density : 42 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: C 97 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7260 (mttm) REVERT: E 77 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8287 (t) REVERT: F 54 THR cc_start: 0.8675 (p) cc_final: 0.8449 (m) REVERT: J 83 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6659 (tt0) outliers start: 31 outliers final: 17 residues processed: 66 average time/residue: 0.6884 time to fit residues: 48.1709 Evaluate side-chains 59 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 E residue 77 VAL Chi-restraints excluded: chain F residue 38 LEU 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 J residue 72 THR 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 53 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.208600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.185443 restraints weight = 4827.566| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 1.81 r_work: 0.4442 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4347 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4230 Z= 0.214 Angle : 0.683 5.885 5720 Z= 0.393 Chirality : 0.058 0.247 760 Planarity : 0.002 0.011 700 Dihedral : 5.466 15.583 610 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 6.74 % Allowed : 18.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.31), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS D 50 PHE 0.011 0.002 PHE E 94 TYR 0.014 0.003 TYR A 39 *********************** 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 68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.458 Fit side-chains REVERT: C 97 LYS cc_start: 0.7530 (mtpt) cc_final: 0.7185 (mttm) REVERT: D 83 GLU cc_start: 0.7495 (tt0) cc_final: 0.7245 (mt-10) REVERT: E 77 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8303 (t) REVERT: F 65 ASN cc_start: 0.7964 (t0) cc_final: 0.7753 (t0) REVERT: I 72 THR cc_start: 0.8314 (p) cc_final: 0.8076 (p) REVERT: J 83 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6706 (tt0) outliers start: 29 outliers final: 20 residues processed: 61 average time/residue: 0.8225 time to fit residues: 52.8926 Evaluate side-chains 59 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 37 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 38 LEU 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 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 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 22 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 = 0.4674 r_free = 0.4674 target = 0.204075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.180450 restraints weight = 4735.430| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 1.80 r_work: 0.4385 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4290 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4230 Z= 0.294 Angle : 0.767 7.232 5720 Z= 0.446 Chirality : 0.060 0.275 760 Planarity : 0.003 0.012 700 Dihedral : 5.684 15.450 610 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.76 % Favored : 84.24 % Rotamer: Outliers : 6.98 % Allowed : 19.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.31), 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 HIS 0.011 0.006 HIS D 50 PHE 0.012 0.003 PHE E 94 TYR 0.014 0.004 TYR A 39 *********************** 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 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 0.667 Fit side-chains REVERT: C 97 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7345 (mttm) REVERT: D 38 LEU cc_start: 0.4471 (OUTLIER) cc_final: 0.4168 (tm) REVERT: D 83 GLU cc_start: 0.7498 (tt0) cc_final: 0.7225 (mt-10) REVERT: F 54 THR cc_start: 0.8734 (p) cc_final: 0.8521 (m) REVERT: H 38 LEU cc_start: 0.5512 (OUTLIER) cc_final: 0.4073 (tp) REVERT: I 72 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7985 (p) REVERT: J 83 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6756 (tt0) outliers start: 30 outliers final: 19 residues processed: 62 average time/residue: 1.1205 time to fit residues: 73.2889 Evaluate side-chains 63 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 54 THR 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 54 THR Chi-restraints excluded: chain E residue 72 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 I residue 80 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 0.0670 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 0.0000 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.6924 ------------------------------------------------------------------------------- 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 = 0.4880 r_free = 0.4880 target = 0.226935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.202414 restraints weight = 4321.251| |-----------------------------------------------------------------------------| r_work (start): 0.4658 rms_B_bonded: 1.90 r_work: 0.4583 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4478 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 4230 Z= 0.124 Angle : 0.540 4.036 5720 Z= 0.305 Chirality : 0.055 0.184 760 Planarity : 0.002 0.008 700 Dihedral : 4.974 13.963 610 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 4.65 % Allowed : 22.56 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.33), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS C 50 PHE 0.009 0.002 PHE E 94 TYR 0.011 0.002 TYR A 39 *********************** 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 61 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.502 Fit side-chains REVERT: C 97 LYS cc_start: 0.7559 (mtpt) cc_final: 0.7245 (mttm) REVERT: D 38 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3383 (tm) REVERT: D 83 GLU cc_start: 0.7364 (tt0) cc_final: 0.7037 (mt-10) REVERT: H 38 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.3860 (tp) outliers start: 20 outliers final: 15 residues processed: 59 average time/residue: 1.2034 time to fit residues: 74.6942 Evaluate side-chains 51 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 62 GLN 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 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain I residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.213039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.189322 restraints weight = 4610.824| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 1.84 r_work: 0.4477 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4379 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4230 Z= 0.198 Angle : 0.622 5.558 5720 Z= 0.360 Chirality : 0.055 0.219 760 Planarity : 0.002 0.012 700 Dihedral : 5.095 13.695 610 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 4.65 % Allowed : 24.19 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.32), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS D 50 PHE 0.027 0.003 PHE G 94 TYR 0.010 0.002 TYR D 39 *********************** 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 61 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.470 Fit side-chains REVERT: C 97 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7224 (mttm) REVERT: D 38 LEU cc_start: 0.3915 (OUTLIER) cc_final: 0.3387 (tm) REVERT: D 83 GLU cc_start: 0.7421 (tt0) cc_final: 0.7146 (mt-10) REVERT: E 77 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8358 (t) REVERT: H 38 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.3687 (tp) outliers start: 20 outliers final: 15 residues processed: 57 average time/residue: 0.9074 time to fit residues: 54.4517 Evaluate side-chains 56 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 62 GLN 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 72 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 = 0.4631 r_free = 0.4631 target = 0.199731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.175640 restraints weight = 4813.374| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 1.83 r_work: 0.4344 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4246 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4230 Z= 0.444 Angle : 0.893 8.699 5720 Z= 0.522 Chirality : 0.064 0.301 760 Planarity : 0.004 0.012 700 Dihedral : 5.996 16.637 610 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.63 % Favored : 82.37 % Rotamer: Outliers : 6.51 % Allowed : 21.86 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.31), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.006 HIS A 50 PHE 0.027 0.003 PHE G 94 TYR 0.016 0.005 TYR C 39 *********************** 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 68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.384 Fit side-chains REVERT: C 97 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7327 (mttm) REVERT: D 83 GLU cc_start: 0.7547 (tt0) cc_final: 0.7302 (mt-10) REVERT: H 38 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.4086 (tp) outliers start: 28 outliers final: 25 residues processed: 61 average time/residue: 0.8501 time to fit residues: 54.6020 Evaluate side-chains 66 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 GLN 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 54 THR 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 E residue 77 VAL 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 I residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.4690 r_free = 0.4690 target = 0.206051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.182256 restraints weight = 4694.649| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 1.83 r_work: 0.4405 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4308 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4230 Z= 0.281 Angle : 0.743 7.166 5720 Z= 0.433 Chirality : 0.059 0.262 760 Planarity : 0.003 0.010 700 Dihedral : 5.679 15.751 610 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 6.05 % Allowed : 22.33 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.31), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS D 50 PHE 0.022 0.003 PHE C 94 TYR 0.014 0.003 TYR C 39 ********************** 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 65 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 39 time to evaluate : 0.456 Fit side-chains REVERT: C 46 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8249 (mt-10) REVERT: C 97 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7317 (mttm) REVERT: D 83 GLU cc_start: 0.7503 (tt0) cc_final: 0.7267 (mt-10) REVERT: H 38 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.3975 (tp) outliers start: 26 outliers final: 21 residues processed: 59 average time/residue: 0.6425 time to fit residues: 40.5936 Evaluate side-chains 61 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 GLN 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 54 THR 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 J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- 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 = 0.4649 r_free = 0.4649 target = 0.201643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.177844 restraints weight = 4752.058| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 1.82 r_work: 0.4369 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4274 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4230 Z= 0.363 Angle : 0.830 8.022 5720 Z= 0.484 Chirality : 0.062 0.289 760 Planarity : 0.003 0.011 700 Dihedral : 5.915 16.354 610 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.14 % Favored : 81.86 % Rotamer: Outliers : 6.05 % Allowed : 22.56 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.31), 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 HIS 0.010 0.005 HIS D 50 PHE 0.024 0.004 PHE C 94 TYR 0.016 0.004 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3127.38 seconds wall clock time: 56 minutes 54.04 seconds (3414.04 seconds total)