Starting phenix.real_space_refine on Tue Feb 3 22:39:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hc7_52039/02_2026/9hc7_52039.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hc7_52039/02_2026/9hc7_52039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hc7_52039/02_2026/9hc7_52039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hc7_52039/02_2026/9hc7_52039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hc7_52039/02_2026/9hc7_52039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hc7_52039/02_2026/9hc7_52039.map" } resolution = 2.85 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= 0.002 sd= 0.016 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 4740 2.51 5 N 1305 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7560 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 504 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 0.70, per 1000 atoms: 0.09 Number of scatterers: 7560 At special positions: 0 Unit cell: (144.9, 140.7, 42, 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 1515 8.00 N 1305 7.00 C 4740 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: 0.72 Conformation dependent library (CDL) restraints added in 215.6 milliseconds 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 63.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.548A pdb=" N VAL A 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA B 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU A 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 16 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA C 19 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LYS C 21 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU B 20 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 16 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA D 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 18 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS D 21 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU C 20 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA E 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU D 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.022A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS C 34 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS D 34 " --> pdb=" O GLU E 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 49 removed outlier: 6.329A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU B 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS A 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL B 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU C 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU D 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU E 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS D 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N VAL E 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 70 through 79 removed outlier: 6.813A pdb=" N VAL B 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY B 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY C 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 74 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 71 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR C 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY D 73 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL C 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL E 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 72 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY E 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 74 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 95 Processing sheet with id=AA8, first strand: chain 'F' and resid 16 through 22 removed outlier: 6.549A pdb=" N VAL F 16 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA G 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA F 18 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LYS G 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU F 20 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL G 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA H 19 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU G 20 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL H 16 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA I 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA H 18 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LYS I 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU H 20 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL I 16 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA J 19 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA I 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LYS J 21 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU I 20 " --> pdb=" O LYS J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 34 through 35 removed outlier: 6.021A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS I 34 " --> pdb=" O GLU J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 38 through 49 removed outlier: 6.329A pdb=" N TYR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER G 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY F 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR G 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU G 46 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS F 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL G 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER I 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU I 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER J 42 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY I 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR J 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU J 46 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS I 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL J 48 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 52 through 57 Processing sheet with id=AB3, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 79 removed outlier: 6.812A pdb=" N VAL G 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR F 72 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY G 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL F 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL H 71 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR G 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY H 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL G 74 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL I 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR H 72 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY I 73 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL H 74 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL J 71 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR I 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY J 73 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL I 74 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 86 through 95 Processing sheet with id=AB6, first strand: chain 'K' and resid 16 through 22 removed outlier: 6.549A pdb=" N VAL K 16 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA L 19 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA K 18 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LYS L 21 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU K 20 " --> pdb=" O LYS L 21 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL L 16 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA M 19 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA L 18 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS M 21 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU L 20 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL M 16 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA N 19 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA M 18 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS N 21 " --> pdb=" O ALA M 18 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU M 20 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL N 16 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA O 19 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA N 18 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LYS O 21 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU N 20 " --> pdb=" O LYS O 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'K' and resid 34 through 35 removed outlier: 6.021A pdb=" N LYS K 34 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS L 34 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS M 34 " --> pdb=" O GLU N 35 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LYS N 34 " --> pdb=" O GLU O 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 38 through 49 removed outlier: 6.330A pdb=" N TYR K 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER L 42 " --> pdb=" O TYR K 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY K 41 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR L 44 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS K 43 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU L 46 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS K 45 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL L 48 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLY K 47 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR L 39 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER M 42 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY L 41 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR M 44 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS L 43 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU M 46 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS L 45 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N VAL M 48 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLY L 47 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR M 39 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER N 42 " --> pdb=" O TYR M 39 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY M 41 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR N 44 " --> pdb=" O GLY M 41 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS M 43 " --> pdb=" O THR N 44 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU N 46 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS M 45 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N VAL N 48 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLY M 47 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR N 39 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N SER O 42 " --> pdb=" O TYR N 39 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY N 41 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR O 44 " --> pdb=" O GLY N 41 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS N 43 " --> pdb=" O THR O 44 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLU O 46 " --> pdb=" O LYS N 43 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYS N 45 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL O 48 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N GLY N 47 " --> pdb=" O VAL O 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'K' and resid 52 through 57 Processing sheet with id=AC1, first strand: chain 'K' and resid 61 through 66 Processing sheet with id=AC2, first strand: chain 'K' and resid 70 through 79 removed outlier: 6.813A pdb=" N VAL L 71 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR K 72 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY L 73 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL K 74 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL M 71 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR L 72 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY M 73 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL L 74 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL N 71 " --> pdb=" O VAL M 70 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR M 72 " --> pdb=" O VAL N 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY N 73 " --> pdb=" O THR M 72 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL M 74 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL O 71 " --> pdb=" O VAL N 70 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR N 72 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY O 73 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL N 74 " --> pdb=" O GLY O 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 86 through 95 288 hydrogen bonds defined for protein. 864 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: 0.92 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.26: 1320 1.26 - 1.34: 1125 1.34 - 1.41: 255 1.41 - 1.48: 1298 1.48 - 1.55: 3577 Bond restraints: 7575 Sorted by residual: bond pdb=" CA GLY C 68 " pdb=" C GLY C 68 " ideal model delta sigma weight residual 1.519 1.475 0.044 1.19e-02 7.06e+03 1.38e+01 bond pdb=" CA GLY M 68 " pdb=" C GLY M 68 " ideal model delta sigma weight residual 1.519 1.475 0.044 1.19e-02 7.06e+03 1.36e+01 bond pdb=" CA GLY G 68 " pdb=" C GLY G 68 " ideal model delta sigma weight residual 1.519 1.475 0.044 1.19e-02 7.06e+03 1.36e+01 bond pdb=" CA GLY H 68 " pdb=" C GLY H 68 " ideal model delta sigma weight residual 1.519 1.475 0.044 1.19e-02 7.06e+03 1.36e+01 bond pdb=" CA GLY K 68 " pdb=" C GLY K 68 " ideal model delta sigma weight residual 1.519 1.475 0.044 1.19e-02 7.06e+03 1.35e+01 ... (remaining 7570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 9046 3.08 - 6.17: 1004 6.17 - 9.25: 119 9.25 - 12.33: 31 12.33 - 15.41: 15 Bond angle restraints: 10215 Sorted by residual: angle pdb=" N VAL B 74 " pdb=" CA VAL B 74 " pdb=" C VAL B 74 " ideal model delta sigma weight residual 110.72 95.31 15.41 1.01e+00 9.80e-01 2.33e+02 angle pdb=" N VAL L 74 " pdb=" CA VAL L 74 " pdb=" C VAL L 74 " ideal model delta sigma weight residual 110.72 95.31 15.41 1.01e+00 9.80e-01 2.33e+02 angle pdb=" N VAL N 74 " pdb=" CA VAL N 74 " pdb=" C VAL N 74 " ideal model delta sigma weight residual 110.72 95.31 15.41 1.01e+00 9.80e-01 2.33e+02 angle pdb=" N VAL H 74 " pdb=" CA VAL H 74 " pdb=" C VAL H 74 " ideal model delta sigma weight residual 110.72 95.32 15.40 1.01e+00 9.80e-01 2.32e+02 angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 110.72 95.32 15.40 1.01e+00 9.80e-01 2.32e+02 ... (remaining 10210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 3780 14.15 - 28.29: 315 28.29 - 42.44: 225 42.44 - 56.58: 105 56.58 - 70.73: 45 Dihedral angle restraints: 4470 sinusoidal: 1500 harmonic: 2970 Sorted by residual: dihedral pdb=" C HIS G 50 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " pdb=" CB HIS G 50 " ideal model delta harmonic sigma weight residual -122.60 -132.29 9.69 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C HIS M 50 " pdb=" N HIS M 50 " pdb=" CA HIS M 50 " pdb=" CB HIS M 50 " ideal model delta harmonic sigma weight residual -122.60 -132.27 9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" C HIS K 50 " pdb=" N HIS K 50 " pdb=" CA HIS K 50 " pdb=" CB HIS K 50 " ideal model delta harmonic sigma weight residual -122.60 -132.26 9.66 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 4467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 995 0.098 - 0.197: 318 0.197 - 0.295: 37 0.295 - 0.393: 0 0.393 - 0.492: 15 Chirality restraints: 1365 Sorted by residual: 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 2.02 0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA HIS E 50 " pdb=" N HIS E 50 " pdb=" C HIS E 50 " pdb=" CB HIS E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA HIS M 50 " pdb=" N HIS M 50 " pdb=" C HIS M 50 " pdb=" CB HIS M 50 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.04e+00 ... (remaining 1362 not shown) Planarity restraints: 1245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 80 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C LYS J 80 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS J 80 " -0.015 2.00e-02 2.50e+03 pdb=" N THR J 81 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 80 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C LYS F 80 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS F 80 " -0.015 2.00e-02 2.50e+03 pdb=" N THR F 81 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 80 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C LYS K 80 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS K 80 " 0.015 2.00e-02 2.50e+03 pdb=" N THR K 81 " 0.013 2.00e-02 2.50e+03 ... (remaining 1242 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 3509 2.92 - 3.41: 6340 3.41 - 3.91: 13563 3.91 - 4.40: 15159 4.40 - 4.90: 27478 Nonbonded interactions: 66049 Sorted by model distance: nonbonded pdb=" N VAL B 74 " pdb=" N THR B 75 " model vdw 2.424 2.560 nonbonded pdb=" N VAL K 74 " pdb=" N THR K 75 " model vdw 2.424 2.560 nonbonded pdb=" N VAL C 74 " pdb=" N THR C 75 " model vdw 2.424 2.560 nonbonded pdb=" N VAL G 74 " pdb=" N THR G 75 " model vdw 2.425 2.560 nonbonded pdb=" N VAL A 74 " pdb=" N THR A 75 " model vdw 2.425 2.560 ... (remaining 66044 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: 0.02 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' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.220 Find NCS groups from input model: 0.040 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.015 0.044 7575 Z= 1.123 Angle : 2.135 15.413 10215 Z= 1.511 Chirality : 0.099 0.492 1365 Planarity : 0.005 0.023 1245 Dihedral : 19.210 70.726 2580 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 31.37 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.28), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.02 (0.21), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.004 TYR B 39 PHE 0.026 0.007 PHE M 94 HIS 0.008 0.005 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.01453 ( 7575) covalent geometry : angle 2.13475 (10215) hydrogen bonds : bond 0.11037 ( 288) hydrogen bonds : angle 8.14140 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.7455 (tttt) cc_final: 0.7247 (tttp) REVERT: D 20 GLU cc_start: 0.8113 (mp0) cc_final: 0.7906 (mp0) REVERT: E 43 LYS cc_start: 0.7777 (mptp) cc_final: 0.6943 (ttpp) REVERT: F 33 THR cc_start: 0.8035 (t) cc_final: 0.7677 (t) REVERT: J 43 LYS cc_start: 0.7953 (mptp) cc_final: 0.7220 (tttt) REVERT: L 20 GLU cc_start: 0.8070 (mp0) cc_final: 0.7709 (mp0) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.4502 time to fit residues: 98.9429 Evaluate side-chains 188 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS D 50 HIS G 50 HIS I 50 HIS L 50 HIS N 50 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.117153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100855 restraints weight = 8943.457| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.97 r_work: 0.3348 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7575 Z= 0.159 Angle : 0.570 7.934 10215 Z= 0.323 Chirality : 0.054 0.125 1365 Planarity : 0.003 0.010 1245 Dihedral : 5.657 21.347 1080 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 8.50 % Allowed : 22.09 % Favored : 69.41 % 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: -1.22 (0.24), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 39 PHE 0.021 0.005 PHE I 94 HIS 0.004 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7575) covalent geometry : angle 0.57030 (10215) hydrogen bonds : bond 0.04300 ( 288) hydrogen bonds : angle 6.48355 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 181 time to evaluate : 0.181 Fit side-chains REVERT: A 43 LYS cc_start: 0.7293 (mptp) cc_final: 0.6137 (ttpp) REVERT: A 57 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: B 43 LYS cc_start: 0.7111 (mptp) cc_final: 0.6892 (mttp) REVERT: C 34 LYS cc_start: 0.8001 (mttt) cc_final: 0.7792 (mtmt) REVERT: C 57 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: D 20 GLU cc_start: 0.8285 (mp0) cc_final: 0.8055 (mp0) REVERT: D 57 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: E 57 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: F 57 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: G 57 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: H 57 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: I 42 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8669 (p) REVERT: I 43 LYS cc_start: 0.7722 (mptp) cc_final: 0.7377 (mptp) REVERT: I 57 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: J 57 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: K 20 GLU cc_start: 0.8188 (mp0) cc_final: 0.7987 (mp0) REVERT: K 34 LYS cc_start: 0.8210 (mttt) cc_final: 0.7985 (mtmt) REVERT: K 57 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: L 20 GLU cc_start: 0.8196 (mp0) cc_final: 0.7804 (mp0) REVERT: L 44 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8616 (t) REVERT: L 45 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8429 (tttm) REVERT: L 57 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: M 57 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: N 20 GLU cc_start: 0.8170 (mp0) cc_final: 0.7969 (mp0) REVERT: O 57 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7682 (tm-30) outliers start: 65 outliers final: 36 residues processed: 223 average time/residue: 0.5024 time to fit residues: 117.9931 Evaluate side-chains 227 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.105255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088819 restraints weight = 9352.902| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.96 r_work: 0.3151 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 7575 Z= 0.367 Angle : 0.659 8.126 10215 Z= 0.375 Chirality : 0.057 0.145 1365 Planarity : 0.003 0.012 1245 Dihedral : 5.886 22.705 1080 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 7.58 % Allowed : 27.32 % Favored : 65.10 % 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: -1.72 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR A 39 PHE 0.021 0.005 PHE N 94 HIS 0.004 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00784 ( 7575) covalent geometry : angle 0.65949 (10215) hydrogen bonds : bond 0.04599 ( 288) hydrogen bonds : angle 6.26384 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: B 21 LYS cc_start: 0.8766 (tttt) cc_final: 0.8404 (tptt) REVERT: B 42 SER cc_start: 0.9031 (t) cc_final: 0.8712 (p) REVERT: B 43 LYS cc_start: 0.7109 (mptp) cc_final: 0.6027 (tttt) REVERT: C 39 TYR cc_start: 0.9397 (m-80) cc_final: 0.9192 (m-80) REVERT: C 43 LYS cc_start: 0.7255 (mptp) cc_final: 0.6835 (mptm) REVERT: C 57 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: D 57 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: E 57 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: F 57 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: G 42 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8706 (p) REVERT: G 57 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: H 21 LYS cc_start: 0.8770 (tttt) cc_final: 0.8562 (tptt) REVERT: H 57 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: I 21 LYS cc_start: 0.8926 (tttt) cc_final: 0.8560 (tptm) REVERT: I 43 LYS cc_start: 0.7635 (mptp) cc_final: 0.7346 (mptp) REVERT: I 57 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: J 43 LYS cc_start: 0.7482 (mptp) cc_final: 0.7238 (mptp) REVERT: J 57 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: K 34 LYS cc_start: 0.8407 (mttt) cc_final: 0.8136 (mtmt) REVERT: K 57 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: L 20 GLU cc_start: 0.8133 (mp0) cc_final: 0.7798 (mp0) REVERT: L 44 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8881 (t) REVERT: L 45 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8511 (tttm) REVERT: M 57 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: N 20 GLU cc_start: 0.8292 (mp0) cc_final: 0.8071 (mp0) REVERT: N 57 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: O 57 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7973 (tm-30) outliers start: 58 outliers final: 32 residues processed: 228 average time/residue: 0.5345 time to fit residues: 128.3071 Evaluate side-chains 239 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 56 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.110897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094617 restraints weight = 9194.407| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.98 r_work: 0.3254 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7575 Z= 0.184 Angle : 0.546 6.558 10215 Z= 0.308 Chirality : 0.052 0.120 1365 Planarity : 0.002 0.009 1245 Dihedral : 5.297 23.312 1080 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 7.45 % Allowed : 26.80 % Favored : 65.75 % 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: -1.92 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR L 39 PHE 0.020 0.005 PHE I 94 HIS 0.002 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7575) covalent geometry : angle 0.54647 (10215) hydrogen bonds : bond 0.03765 ( 288) hydrogen bonds : angle 5.95242 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 0.286 Fit side-chains REVERT: A 57 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: B 21 LYS cc_start: 0.8732 (tttt) cc_final: 0.8373 (tptt) REVERT: B 43 LYS cc_start: 0.7081 (mptp) cc_final: 0.6021 (tttt) REVERT: B 57 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: C 39 TYR cc_start: 0.9372 (m-80) cc_final: 0.9158 (m-80) REVERT: C 57 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: D 43 LYS cc_start: 0.7372 (mptp) cc_final: 0.7141 (mptp) REVERT: D 57 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: E 57 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: F 34 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8601 (mtmt) REVERT: F 57 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: F 58 LYS cc_start: 0.9127 (mttp) cc_final: 0.8786 (mttt) REVERT: G 42 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8752 (p) REVERT: G 57 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: H 21 LYS cc_start: 0.8753 (tttt) cc_final: 0.8525 (tptt) REVERT: H 57 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: I 21 LYS cc_start: 0.8824 (tttt) cc_final: 0.8437 (tptm) REVERT: I 43 LYS cc_start: 0.7672 (mptp) cc_final: 0.6555 (tttt) REVERT: I 57 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: J 43 LYS cc_start: 0.7289 (mptp) cc_final: 0.7061 (mptp) REVERT: J 57 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: K 34 LYS cc_start: 0.8317 (mttt) cc_final: 0.8082 (mtmt) REVERT: K 57 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: K 58 LYS cc_start: 0.9105 (mttp) cc_final: 0.8623 (mttt) REVERT: L 20 GLU cc_start: 0.8131 (mp0) cc_final: 0.7762 (mp0) REVERT: L 21 LYS cc_start: 0.8751 (tttt) cc_final: 0.8503 (tptm) REVERT: L 44 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8753 (t) REVERT: L 45 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8418 (tttm) REVERT: L 57 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: M 45 LYS cc_start: 0.8899 (ttpp) cc_final: 0.7778 (mptp) REVERT: M 57 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: N 15 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.8020 (t) REVERT: N 20 GLU cc_start: 0.8183 (mp0) cc_final: 0.7975 (mp0) REVERT: N 57 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: O 57 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7807 (tm-30) outliers start: 57 outliers final: 27 residues processed: 233 average time/residue: 0.4878 time to fit residues: 119.6155 Evaluate side-chains 236 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.108003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.091678 restraints weight = 9293.767| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.97 r_work: 0.3210 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7575 Z= 0.238 Angle : 0.567 6.652 10215 Z= 0.321 Chirality : 0.053 0.121 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.321 24.990 1080 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 8.24 % Allowed : 26.93 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR L 39 PHE 0.020 0.004 PHE N 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 7575) covalent geometry : angle 0.56670 (10215) hydrogen bonds : bond 0.03882 ( 288) hydrogen bonds : angle 5.84985 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.278 Fit side-chains REVERT: A 57 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: B 21 LYS cc_start: 0.8775 (tttt) cc_final: 0.8358 (tptt) REVERT: B 42 SER cc_start: 0.9024 (t) cc_final: 0.8709 (p) REVERT: B 43 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6077 (tttt) REVERT: B 57 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: C 39 TYR cc_start: 0.9393 (m-80) cc_final: 0.9182 (m-80) REVERT: C 57 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: D 43 LYS cc_start: 0.7414 (mptp) cc_final: 0.7171 (mptp) REVERT: D 44 THR cc_start: 0.8964 (t) cc_final: 0.8634 (t) REVERT: D 57 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: E 57 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: F 57 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: F 58 LYS cc_start: 0.9149 (mttp) cc_final: 0.8863 (mttt) REVERT: G 21 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8461 (tptt) REVERT: G 34 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7562 (mtmt) REVERT: G 42 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8756 (p) REVERT: G 57 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: H 57 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: I 21 LYS cc_start: 0.8837 (tttt) cc_final: 0.8458 (tptm) REVERT: I 43 LYS cc_start: 0.7641 (mptp) cc_final: 0.6583 (tttt) REVERT: I 57 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: J 43 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7230 (mptp) REVERT: J 45 LYS cc_start: 0.8856 (tttm) cc_final: 0.7977 (mptp) REVERT: J 57 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: K 34 LYS cc_start: 0.8372 (mttt) cc_final: 0.8111 (mtmt) REVERT: K 57 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: L 15 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7756 (t) REVERT: L 20 GLU cc_start: 0.8152 (mp0) cc_final: 0.7738 (mp0) REVERT: L 21 LYS cc_start: 0.8665 (tttt) cc_final: 0.8419 (tptm) REVERT: L 44 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8797 (t) REVERT: L 45 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8501 (tttm) REVERT: L 57 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: M 57 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: N 15 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.8003 (t) REVERT: N 20 GLU cc_start: 0.8185 (mp0) cc_final: 0.7983 (mp0) REVERT: N 57 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: O 57 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7965 (tm-30) outliers start: 63 outliers final: 31 residues processed: 228 average time/residue: 0.4589 time to fit residues: 110.2108 Evaluate side-chains 242 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.105370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088979 restraints weight = 9365.156| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.97 r_work: 0.3236 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 7575 Z= 0.319 Angle : 0.616 7.084 10215 Z= 0.349 Chirality : 0.054 0.127 1365 Planarity : 0.003 0.010 1245 Dihedral : 5.451 26.610 1080 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 8.10 % Allowed : 26.54 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.003 TYR L 39 PHE 0.020 0.005 PHE N 94 HIS 0.004 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 7575) covalent geometry : angle 0.61624 (10215) hydrogen bonds : bond 0.04046 ( 288) hydrogen bonds : angle 5.87642 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 0.270 Fit side-chains REVERT: A 34 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8236 (mtmt) REVERT: A 57 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: B 21 LYS cc_start: 0.8765 (tttt) cc_final: 0.8346 (tptt) REVERT: B 43 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6114 (tttt) REVERT: B 57 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: C 57 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: D 43 LYS cc_start: 0.7569 (mptp) cc_final: 0.7345 (mptp) REVERT: D 44 THR cc_start: 0.9012 (t) cc_final: 0.8685 (t) REVERT: D 57 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: E 57 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: F 57 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: F 58 LYS cc_start: 0.9129 (mttp) cc_final: 0.8879 (mttt) REVERT: G 34 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7632 (mtmt) REVERT: G 42 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8708 (p) REVERT: G 57 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: H 57 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: I 21 LYS cc_start: 0.8869 (tttt) cc_final: 0.8482 (tptm) REVERT: I 43 LYS cc_start: 0.7731 (mptp) cc_final: 0.6703 (tttt) REVERT: I 57 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: J 43 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7302 (mptp) REVERT: J 57 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: K 34 LYS cc_start: 0.8425 (mttt) cc_final: 0.8111 (mtmt) REVERT: K 57 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7727 (tm-30) REVERT: L 15 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7802 (t) REVERT: L 20 GLU cc_start: 0.8195 (mp0) cc_final: 0.7804 (mp0) REVERT: L 44 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8897 (t) REVERT: L 45 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8543 (tttm) REVERT: L 57 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: M 57 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: N 57 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: O 23 LYS cc_start: 0.8188 (tttm) cc_final: 0.7981 (ttpt) REVERT: O 57 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8001 (tm-30) outliers start: 62 outliers final: 32 residues processed: 232 average time/residue: 0.4572 time to fit residues: 111.6007 Evaluate side-chains 253 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 overall best weight: 4.0786 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.108427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.092185 restraints weight = 9309.857| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.97 r_work: 0.3291 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7575 Z= 0.225 Angle : 0.558 6.365 10215 Z= 0.316 Chirality : 0.052 0.124 1365 Planarity : 0.002 0.009 1245 Dihedral : 5.202 26.164 1080 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 7.06 % Allowed : 26.93 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.003 TYR L 39 PHE 0.019 0.004 PHE N 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 7575) covalent geometry : angle 0.55812 (10215) hydrogen bonds : bond 0.03668 ( 288) hydrogen bonds : angle 5.75948 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.234 Fit side-chains REVERT: A 57 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: B 21 LYS cc_start: 0.8756 (tttt) cc_final: 0.8345 (tptt) REVERT: B 43 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6057 (tttt) REVERT: B 57 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: C 43 LYS cc_start: 0.7047 (mptp) cc_final: 0.6720 (mptm) REVERT: C 57 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: D 44 THR cc_start: 0.8898 (t) cc_final: 0.8543 (t) REVERT: D 57 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: E 57 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: F 57 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: F 58 LYS cc_start: 0.9147 (mttp) cc_final: 0.8838 (mttm) REVERT: G 34 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7601 (mtmt) REVERT: G 42 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8741 (p) REVERT: G 57 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: H 57 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: I 21 LYS cc_start: 0.8938 (tttt) cc_final: 0.8499 (tttm) REVERT: I 43 LYS cc_start: 0.7692 (mptp) cc_final: 0.6643 (tttt) REVERT: I 57 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: J 43 LYS cc_start: 0.7517 (mptp) cc_final: 0.7295 (mptp) REVERT: J 45 LYS cc_start: 0.8854 (tttm) cc_final: 0.7967 (mptp) REVERT: J 57 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: K 34 LYS cc_start: 0.8388 (mttt) cc_final: 0.8111 (mtmt) REVERT: K 57 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: L 15 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7754 (t) REVERT: L 20 GLU cc_start: 0.8195 (mp0) cc_final: 0.7793 (mp0) REVERT: L 45 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7779 (mptm) REVERT: L 57 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: M 43 LYS cc_start: 0.7331 (mptp) cc_final: 0.6137 (tttp) REVERT: M 45 LYS cc_start: 0.8957 (ttpp) cc_final: 0.7867 (mptp) REVERT: M 57 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: N 57 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: O 57 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7898 (tm-30) outliers start: 54 outliers final: 29 residues processed: 233 average time/residue: 0.4586 time to fit residues: 112.5859 Evaluate side-chains 246 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.103958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087448 restraints weight = 9477.808| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.01 r_work: 0.3208 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 7575 Z= 0.364 Angle : 0.646 7.583 10215 Z= 0.366 Chirality : 0.055 0.140 1365 Planarity : 0.003 0.010 1245 Dihedral : 5.465 27.040 1080 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 7.19 % Allowed : 27.06 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.003 TYR L 39 PHE 0.020 0.005 PHE N 94 HIS 0.004 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00769 ( 7575) covalent geometry : angle 0.64631 (10215) hydrogen bonds : bond 0.04063 ( 288) hydrogen bonds : angle 5.81358 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 0.186 Fit side-chains REVERT: A 34 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8329 (mtmt) REVERT: A 57 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: B 21 LYS cc_start: 0.8755 (tttt) cc_final: 0.8335 (tptt) REVERT: B 43 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6096 (tttt) REVERT: B 57 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: C 57 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: D 20 GLU cc_start: 0.8258 (mp0) cc_final: 0.8017 (mp0) REVERT: D 44 THR cc_start: 0.9031 (t) cc_final: 0.8680 (t) REVERT: D 57 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: D 58 LYS cc_start: 0.9127 (mttp) cc_final: 0.8628 (mttp) REVERT: E 57 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: F 34 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8522 (mtmt) REVERT: F 57 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: G 34 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.7633 (mtmt) REVERT: G 42 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8720 (p) REVERT: G 57 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: H 57 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: I 21 LYS cc_start: 0.8939 (tttt) cc_final: 0.8543 (tptm) REVERT: I 43 LYS cc_start: 0.7741 (mptp) cc_final: 0.6670 (tttt) REVERT: I 57 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: J 43 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7391 (mptp) REVERT: J 45 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.7994 (mptp) REVERT: J 57 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: K 34 LYS cc_start: 0.8436 (mttt) cc_final: 0.8093 (mtmt) REVERT: K 57 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: L 15 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7787 (t) REVERT: L 20 GLU cc_start: 0.8232 (mp0) cc_final: 0.7859 (mp0) REVERT: L 45 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.7727 (mptm) REVERT: L 57 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: M 45 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8669 (tttp) REVERT: M 57 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: N 34 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7358 (mtmt) REVERT: O 57 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8013 (tm-30) outliers start: 55 outliers final: 29 residues processed: 241 average time/residue: 0.4616 time to fit residues: 116.9601 Evaluate side-chains 261 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 34 LYS Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.107341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090885 restraints weight = 9254.744| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.00 r_work: 0.3285 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7575 Z= 0.250 Angle : 0.583 6.666 10215 Z= 0.328 Chirality : 0.053 0.126 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.225 26.463 1080 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 7.06 % Allowed : 27.84 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.003 TYR L 39 PHE 0.019 0.004 PHE N 94 HIS 0.003 0.001 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 7575) covalent geometry : angle 0.58343 (10215) hydrogen bonds : bond 0.03707 ( 288) hydrogen bonds : angle 5.73353 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.243 Fit side-chains REVERT: A 23 LYS cc_start: 0.7750 (tmtt) cc_final: 0.7490 (ttpt) REVERT: A 34 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8417 (mtmt) REVERT: A 57 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: B 21 LYS cc_start: 0.8805 (tttt) cc_final: 0.8399 (tptt) REVERT: B 43 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6144 (tttt) REVERT: B 57 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: C 43 LYS cc_start: 0.7229 (mptp) cc_final: 0.6903 (mptm) REVERT: C 57 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: D 44 THR cc_start: 0.9060 (t) cc_final: 0.8700 (t) REVERT: D 57 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: E 57 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: F 34 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8593 (mtmt) REVERT: F 57 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: G 34 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.7577 (mtmt) REVERT: G 57 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: H 57 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: I 21 LYS cc_start: 0.8959 (tttt) cc_final: 0.8546 (tttm) REVERT: I 43 LYS cc_start: 0.7782 (mptp) cc_final: 0.6741 (tttt) REVERT: I 57 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: J 43 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7335 (mptp) REVERT: J 45 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8017 (mptp) REVERT: J 57 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: K 34 LYS cc_start: 0.8508 (mttt) cc_final: 0.8200 (mtmt) REVERT: K 57 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: L 15 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7808 (t) REVERT: L 20 GLU cc_start: 0.8238 (mp0) cc_final: 0.7883 (mp0) REVERT: L 45 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7803 (mptm) REVERT: L 57 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: M 43 LYS cc_start: 0.7441 (mptp) cc_final: 0.6230 (tttp) REVERT: M 45 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8688 (tttp) REVERT: M 57 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: O 57 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8054 (tm-30) outliers start: 54 outliers final: 31 residues processed: 235 average time/residue: 0.4528 time to fit residues: 112.0168 Evaluate side-chains 255 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.106011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089655 restraints weight = 9352.926| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.98 r_work: 0.3263 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 7575 Z= 0.295 Angle : 0.614 7.505 10215 Z= 0.346 Chirality : 0.054 0.128 1365 Planarity : 0.003 0.012 1245 Dihedral : 5.307 26.687 1080 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 7.06 % Allowed : 27.71 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.004 TYR L 39 PHE 0.019 0.004 PHE N 94 HIS 0.004 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00615 ( 7575) covalent geometry : angle 0.61398 (10215) hydrogen bonds : bond 0.03869 ( 288) hydrogen bonds : angle 5.74450 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.263 Fit side-chains REVERT: A 57 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: B 21 LYS cc_start: 0.8752 (tttt) cc_final: 0.8334 (tptt) REVERT: B 43 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6173 (tttt) REVERT: B 57 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: C 57 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: D 44 THR cc_start: 0.9085 (t) cc_final: 0.8804 (t) REVERT: D 57 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: D 58 LYS cc_start: 0.9111 (mttp) cc_final: 0.8612 (mttp) REVERT: E 57 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: F 34 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8513 (mtmt) REVERT: F 57 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: F 58 LYS cc_start: 0.9163 (mttp) cc_final: 0.8883 (mttt) REVERT: G 34 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7566 (mtmt) REVERT: G 57 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: H 57 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: I 21 LYS cc_start: 0.8932 (tttt) cc_final: 0.8640 (tttt) REVERT: I 43 LYS cc_start: 0.7724 (mptp) cc_final: 0.6656 (tttt) REVERT: I 57 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: J 43 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7302 (mptp) REVERT: J 45 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.7972 (mptp) REVERT: J 57 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: K 34 LYS cc_start: 0.8495 (mttt) cc_final: 0.8167 (mtmt) REVERT: K 57 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: L 15 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7790 (t) REVERT: L 20 GLU cc_start: 0.8224 (mp0) cc_final: 0.7855 (mp0) REVERT: L 45 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7711 (mptm) REVERT: L 57 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: M 57 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: N 34 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7352 (mtmt) REVERT: O 57 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8051 (tm-30) outliers start: 54 outliers final: 31 residues processed: 240 average time/residue: 0.4551 time to fit residues: 114.9521 Evaluate side-chains 263 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 57 GLU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 34 LYS Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 57 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.104319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087926 restraints weight = 9377.227| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.99 r_work: 0.3237 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 7575 Z= 0.366 Angle : 0.665 8.036 10215 Z= 0.373 Chirality : 0.056 0.139 1365 Planarity : 0.003 0.011 1245 Dihedral : 5.439 27.111 1080 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 7.06 % Allowed : 27.97 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.004 TYR L 39 PHE 0.020 0.005 PHE N 94 HIS 0.005 0.002 HIS L 50 Details of bonding type rmsd covalent geometry : bond 0.00771 ( 7575) covalent geometry : angle 0.66450 (10215) hydrogen bonds : bond 0.04038 ( 288) hydrogen bonds : angle 5.80506 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2533.30 seconds wall clock time: 43 minutes 59.09 seconds (2639.09 seconds total)