Starting phenix.real_space_refine on Tue Feb 3 22:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hca_52042/02_2026/9hca_52042.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hca_52042/02_2026/9hca_52042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hca_52042/02_2026/9hca_52042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hca_52042/02_2026/9hca_52042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hca_52042/02_2026/9hca_52042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hca_52042/02_2026/9hca_52042.map" } resolution = 2.7 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= 0.014 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): 0.00s 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: 0.77, per 1000 atoms: 0.10 Number of scatterers: 7560 At special positions: 0 Unit cell: (145.95, 139.65, 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: 0.52 Conformation dependent library (CDL) restraints added in 256.3 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: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.551A pdb=" N VAL A 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA B 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.337A 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: 7.965A pdb=" N ALA C 19 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 7.951A 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: 7.992A pdb=" N ALA D 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA C 18 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LYS D 21 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.347A 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: 6.466A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 7.964A 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: 6.021A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.025A 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: 7.760A 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: 6.321A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU B 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 7.204A 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: 9.005A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.333A 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: 6.359A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 7.924A 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: 7.032A 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: 9.006A 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: 6.316A 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: 7.199A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 9.002A 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: 6.352A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.323A 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: 9.005A 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: 6.813A pdb=" N THR A 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY B 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL C 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY C 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.521A 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: 6.796A pdb=" N GLY D 73 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.527A 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: 6.809A pdb=" N THR D 72 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY E 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.524A 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: 6.551A pdb=" N VAL F 16 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA G 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 18 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS G 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU F 20 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL G 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 7.979A 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: 7.963A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 6.330A 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: 7.978A pdb=" N ALA I 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA H 18 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LYS I 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 6.331A 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: 6.468A pdb=" N ALA I 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LYS J 21 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 6.329A 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: 6.022A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 6.025A 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: 6.328A pdb=" N TYR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 7.760A 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: 6.321A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU G 46 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS F 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N VAL G 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 7.761A 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: 7.918A 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: 9.006A 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: 7.761A pdb=" N SER I 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU I 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 9.005A 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: 7.761A 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: 7.918A 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: 7.205A pdb=" N LYS I 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N VAL J 48 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 9.005A 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: 6.813A pdb=" N VAL G 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR F 72 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY G 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.524A 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: 6.809A pdb=" N THR G 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY H 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL G 74 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL I 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.809A 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: 6.809A pdb=" N VAL J 71 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR I 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.789A 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: 6.551A pdb=" N VAL K 16 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA L 19 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA K 18 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS L 21 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU K 20 " --> pdb=" O LYS L 21 " (cutoff:3.500A) removed outlier: 6.542A 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: 6.467A pdb=" N ALA L 18 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LYS M 21 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU L 20 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 6.542A 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: 6.468A pdb=" N ALA M 18 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LYS N 21 " --> pdb=" O ALA M 18 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU M 20 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 6.539A 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: 6.465A pdb=" N ALA N 18 " --> pdb=" O ALA O 19 " (cutoff:3.500A) removed outlier: 7.960A 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: 6.025A pdb=" N LYS L 34 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS M 34 " --> pdb=" O GLU N 35 " (cutoff:3.500A) removed outlier: 6.025A 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: 6.329A 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: 7.916A pdb=" N THR L 44 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS K 43 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU L 46 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 7.203A 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: 9.005A pdb=" N GLY K 47 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR L 39 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER M 42 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 6.352A 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: 6.322A pdb=" N LYS L 43 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU M 46 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 7.206A 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: 9.005A 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: 7.761A 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: 6.323A 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: 7.205A 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: 9.005A 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: 7.918A pdb=" N THR O 44 " --> pdb=" O GLY N 41 " (cutoff:3.500A) removed outlier: 6.325A 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: 7.208A 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: 9.007A 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: 6.813A pdb=" N THR K 72 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY L 73 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL K 74 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL M 71 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR L 72 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY M 73 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 6.524A 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: 6.810A pdb=" N THR M 72 " --> pdb=" O VAL N 71 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY N 73 " --> pdb=" O THR M 72 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL M 74 " --> pdb=" O GLY N 73 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL O 71 " --> pdb=" O VAL N 70 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR N 72 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY O 73 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 6.525A 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: 1.06 Time building geometry restraints manager: 0.68 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: 1305 1.48 - 1.55: 3570 Bond restraints: 7575 Sorted by residual: bond pdb=" CA GLY B 68 " pdb=" C GLY B 68 " ideal model delta sigma weight residual 1.519 1.475 0.044 1.19e-02 7.06e+03 1.39e+01 bond pdb=" CA GLY I 68 " pdb=" C GLY I 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 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 1.38e+01 bond pdb=" CA GLY N 68 " pdb=" C GLY N 68 " ideal model delta sigma weight residual 1.519 1.475 0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" CA GLY A 68 " pdb=" C GLY A 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: 9057 3.08 - 6.16: 993 6.16 - 9.23: 120 9.23 - 12.31: 30 12.31 - 15.39: 15 Bond angle restraints: 10215 Sorted by residual: angle pdb=" N VAL N 74 " pdb=" CA VAL N 74 " pdb=" C VAL N 74 " ideal model delta sigma weight residual 110.72 95.33 15.39 1.01e+00 9.80e-01 2.32e+02 angle pdb=" N VAL M 74 " pdb=" CA VAL M 74 " pdb=" C VAL M 74 " ideal model delta sigma weight residual 110.72 95.33 15.39 1.01e+00 9.80e-01 2.32e+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 95.33 15.39 1.01e+00 9.80e-01 2.32e+02 angle pdb=" N VAL C 74 " pdb=" CA VAL C 74 " pdb=" C VAL C 74 " ideal model delta sigma weight residual 110.72 95.35 15.37 1.01e+00 9.80e-01 2.32e+02 angle pdb=" N VAL G 74 " pdb=" CA VAL G 74 " pdb=" C VAL G 74 " ideal model delta sigma weight residual 110.72 95.36 15.36 1.01e+00 9.80e-01 2.31e+02 ... (remaining 10210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.67: 3749 14.67 - 29.34: 376 29.34 - 44.01: 225 44.01 - 58.68: 60 58.68 - 73.34: 60 Dihedral angle restraints: 4470 sinusoidal: 1500 harmonic: 2970 Sorted by residual: dihedral pdb=" C HIS B 50 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " pdb=" CB HIS B 50 " ideal model delta harmonic sigma weight residual -122.60 -132.36 9.76 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" C HIS J 50 " pdb=" N HIS J 50 " pdb=" CA HIS J 50 " pdb=" CB HIS J 50 " ideal model delta harmonic sigma weight residual -122.60 -132.34 9.74 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" C HIS L 50 " pdb=" N HIS L 50 " pdb=" CA HIS L 50 " pdb=" CB HIS L 50 " ideal model delta harmonic sigma weight residual -122.60 -132.32 9.72 0 2.50e+00 1.60e-01 1.51e+01 ... (remaining 4467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1004 0.100 - 0.199: 318 0.199 - 0.299: 28 0.299 - 0.398: 0 0.398 - 0.498: 15 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA HIS B 50 " pdb=" N HIS B 50 " pdb=" C HIS B 50 " pdb=" CB HIS B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CA HIS J 50 " pdb=" N HIS J 50 " pdb=" C HIS J 50 " pdb=" CB HIS J 50 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" CA HIS C 50 " pdb=" N HIS C 50 " pdb=" C HIS C 50 " pdb=" CB HIS C 50 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.14e+00 ... (remaining 1362 not shown) Planarity restraints: 1245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 80 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C LYS G 80 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS G 80 " -0.015 2.00e-02 2.50e+03 pdb=" N THR G 81 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 80 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C LYS N 80 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS N 80 " 0.015 2.00e-02 2.50e+03 pdb=" N THR N 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 2.27e-02 5.15e+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 ... (remaining 1242 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 3509 2.92 - 3.41: 6409 3.41 - 3.91: 13165 3.91 - 4.40: 15266 4.40 - 4.90: 27255 Nonbonded interactions: 65604 Sorted by model distance: nonbonded pdb=" N VAL N 74 " pdb=" N THR N 75 " model vdw 2.423 2.560 nonbonded pdb=" N VAL M 74 " pdb=" N THR M 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 O 74 " pdb=" N THR O 75 " model vdw 2.424 2.560 nonbonded pdb=" N VAL G 74 " pdb=" N THR G 75 " model vdw 2.424 2.560 ... (remaining 65599 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.270 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.045 7575 Z= 1.121 Angle : 2.123 15.390 10215 Z= 1.503 Chirality : 0.099 0.498 1365 Planarity : 0.005 0.023 1245 Dihedral : 19.390 73.344 2580 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.07 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 N 39 PHE 0.026 0.007 PHE O 94 HIS 0.008 0.005 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.01452 ( 7575) covalent geometry : angle 2.12340 (10215) hydrogen bonds : bond 0.11006 ( 288) hydrogen bonds : angle 8.11746 ( 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 274 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.278 Fit side-chains REVERT: A 35 GLU cc_start: 0.7563 (tt0) cc_final: 0.7345 (tm-30) REVERT: B 35 GLU cc_start: 0.7470 (tt0) cc_final: 0.7006 (tm-30) REVERT: B 57 GLU cc_start: 0.7914 (tt0) cc_final: 0.7711 (tt0) REVERT: C 35 GLU cc_start: 0.7523 (tt0) cc_final: 0.7228 (tm-30) REVERT: D 35 GLU cc_start: 0.7507 (tt0) cc_final: 0.7156 (tm-30) REVERT: E 35 GLU cc_start: 0.7647 (tt0) cc_final: 0.7437 (tm-30) REVERT: E 57 GLU cc_start: 0.8195 (tt0) cc_final: 0.7957 (tt0) REVERT: F 35 GLU cc_start: 0.7644 (tt0) cc_final: 0.7341 (tm-30) REVERT: G 35 GLU cc_start: 0.7364 (tt0) cc_final: 0.7007 (tm-30) REVERT: H 35 GLU cc_start: 0.7545 (tt0) cc_final: 0.7236 (tm-30) REVERT: I 35 GLU cc_start: 0.7635 (tt0) cc_final: 0.7184 (tm-30) REVERT: I 46 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7579 (mt-10) REVERT: I 57 GLU cc_start: 0.7809 (tt0) cc_final: 0.7526 (tt0) REVERT: J 35 GLU cc_start: 0.7593 (tt0) cc_final: 0.7286 (tm-30) REVERT: K 35 GLU cc_start: 0.7559 (tt0) cc_final: 0.7341 (tm-30) REVERT: L 35 GLU cc_start: 0.7527 (tt0) cc_final: 0.7176 (tm-30) REVERT: L 46 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7458 (mt-10) REVERT: N 35 GLU cc_start: 0.7479 (tt0) cc_final: 0.7231 (tm-30) REVERT: N 46 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7480 (mt-10) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.5155 time to fit residues: 148.5795 Evaluate side-chains 241 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.0870 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN D 50 HIS I 50 HIS K 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.116200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097493 restraints weight = 8453.508| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.19 r_work: 0.3385 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7575 Z= 0.232 Angle : 0.663 8.445 10215 Z= 0.366 Chirality : 0.056 0.134 1365 Planarity : 0.003 0.011 1245 Dihedral : 5.895 23.422 1080 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.49 % Allowed : 24.18 % Favored : 70.33 % 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: -1.40 (0.23), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR N 39 PHE 0.023 0.005 PHE N 94 HIS 0.005 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 7575) covalent geometry : angle 0.66278 (10215) hydrogen bonds : bond 0.04421 ( 288) hydrogen bonds : angle 6.13111 ( 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 222 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.266 Fit side-chains REVERT: A 23 LYS cc_start: 0.7383 (tmtt) cc_final: 0.7146 (tptt) REVERT: A 34 LYS cc_start: 0.8139 (mttt) cc_final: 0.7874 (mttt) REVERT: C 23 LYS cc_start: 0.7133 (tmtt) cc_final: 0.6919 (tptt) REVERT: E 35 GLU cc_start: 0.8127 (tt0) cc_final: 0.7500 (tm-30) REVERT: F 34 LYS cc_start: 0.8133 (mttt) cc_final: 0.7803 (mtmt) REVERT: F 43 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8392 (ttmm) REVERT: G 15 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7918 (t) REVERT: G 34 LYS cc_start: 0.8077 (mttt) cc_final: 0.7824 (mttt) REVERT: G 35 GLU cc_start: 0.7984 (tt0) cc_final: 0.7270 (tm-30) REVERT: H 35 GLU cc_start: 0.8010 (tt0) cc_final: 0.7362 (tm-30) REVERT: I 15 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7727 (t) REVERT: I 57 GLU cc_start: 0.8358 (tt0) cc_final: 0.8136 (tt0) REVERT: J 35 GLU cc_start: 0.8051 (tt0) cc_final: 0.7460 (tm-30) REVERT: K 23 LYS cc_start: 0.7332 (tmtt) cc_final: 0.7094 (tptt) REVERT: L 15 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7962 (t) REVERT: M 43 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8380 (tttm) outliers start: 42 outliers final: 31 residues processed: 199 average time/residue: 0.4795 time to fit residues: 100.5762 Evaluate side-chains 209 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR 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 K residue 15 VAL 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 M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 63 optimal weight: 0.3980 chunk 59 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.109052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090537 restraints weight = 8760.897| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.21 r_work: 0.3315 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 7575 Z= 0.309 Angle : 0.661 7.550 10215 Z= 0.364 Chirality : 0.055 0.139 1365 Planarity : 0.003 0.011 1245 Dihedral : 5.875 23.616 1080 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 6.67 % Allowed : 24.84 % Favored : 68.50 % 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: -1.62 (0.23), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR L 39 PHE 0.023 0.005 PHE N 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 7575) covalent geometry : angle 0.66108 (10215) hydrogen bonds : bond 0.04223 ( 288) hydrogen bonds : angle 5.84763 ( 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 232 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.285 Fit side-chains REVERT: A 34 LYS cc_start: 0.8181 (mttt) cc_final: 0.7949 (mttt) REVERT: C 23 LYS cc_start: 0.7258 (tmtt) cc_final: 0.6996 (tptt) REVERT: C 80 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8699 (mttm) REVERT: F 34 LYS cc_start: 0.8206 (mttt) cc_final: 0.7893 (mtmt) REVERT: F 43 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8532 (ttmm) REVERT: F 61 GLU cc_start: 0.8067 (mp0) cc_final: 0.7335 (tt0) REVERT: G 15 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7903 (t) REVERT: G 35 GLU cc_start: 0.8052 (tt0) cc_final: 0.7232 (tm-30) REVERT: H 35 GLU cc_start: 0.8112 (tt0) cc_final: 0.7418 (tm-30) REVERT: J 35 GLU cc_start: 0.8137 (tt0) cc_final: 0.7492 (tm-30) REVERT: K 45 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8809 (ttpp) REVERT: L 15 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8312 (t) outliers start: 51 outliers final: 40 residues processed: 204 average time/residue: 0.5150 time to fit residues: 110.4478 Evaluate side-chains 221 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 44 THR 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 N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR 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: 10.0000 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093145 restraints weight = 8964.528| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.24 r_work: 0.3294 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4331 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= 0.330 Angle : 0.660 7.079 10215 Z= 0.363 Chirality : 0.055 0.138 1365 Planarity : 0.002 0.011 1245 Dihedral : 5.771 23.705 1080 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 6.41 % Allowed : 24.97 % 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: -1.87 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 39 PHE 0.022 0.005 PHE D 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 7575) covalent geometry : angle 0.65971 (10215) hydrogen bonds : bond 0.03954 ( 288) hydrogen bonds : angle 5.69060 ( 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 233 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.340 Fit side-chains REVERT: A 34 LYS cc_start: 0.8176 (mttt) cc_final: 0.7962 (mttt) REVERT: C 23 LYS cc_start: 0.7463 (tmtt) cc_final: 0.7189 (tptt) REVERT: F 43 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8532 (ttmm) REVERT: F 61 GLU cc_start: 0.8237 (mp0) cc_final: 0.7455 (tt0) REVERT: G 35 GLU cc_start: 0.8087 (tt0) cc_final: 0.7256 (tm-30) REVERT: H 35 GLU cc_start: 0.8105 (tt0) cc_final: 0.7418 (tm-30) REVERT: J 34 LYS cc_start: 0.8573 (mttt) cc_final: 0.8341 (mtpt) REVERT: J 35 GLU cc_start: 0.8158 (tt0) cc_final: 0.7486 (tm-30) REVERT: L 80 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8684 (mttm) REVERT: M 34 LYS cc_start: 0.8063 (mttt) cc_final: 0.7838 (mttt) REVERT: N 42 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8757 (p) outliers start: 49 outliers final: 38 residues processed: 204 average time/residue: 0.5525 time to fit residues: 118.1431 Evaluate side-chains 223 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 80 LYS 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 N residue 42 SER Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 0.0000 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 overall best weight: 5.1790 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.112624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.094441 restraints weight = 8890.435| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.24 r_work: 0.3315 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 7575 Z= 0.277 Angle : 0.630 6.683 10215 Z= 0.345 Chirality : 0.054 0.138 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.538 23.419 1080 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 6.80 % Allowed : 25.88 % Favored : 67.32 % 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: -2.07 (0.22), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.022 0.005 PHE D 94 HIS 0.003 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 7575) covalent geometry : angle 0.63004 (10215) hydrogen bonds : bond 0.03666 ( 288) hydrogen bonds : angle 5.60126 ( 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 237 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 0.265 Fit side-chains REVERT: A 34 LYS cc_start: 0.8241 (mttt) cc_final: 0.8014 (mttt) REVERT: C 23 LYS cc_start: 0.7409 (tmtt) cc_final: 0.7166 (tptt) REVERT: E 35 GLU cc_start: 0.8116 (tt0) cc_final: 0.7435 (tm-30) REVERT: F 43 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8510 (ttmm) REVERT: F 61 GLU cc_start: 0.8216 (mp0) cc_final: 0.7443 (tt0) REVERT: H 35 GLU cc_start: 0.8101 (tt0) cc_final: 0.7423 (tm-30) REVERT: J 34 LYS cc_start: 0.8551 (mttt) cc_final: 0.8314 (mtpt) REVERT: J 35 GLU cc_start: 0.8136 (tt0) cc_final: 0.7507 (tm-30) REVERT: J 57 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: L 80 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8643 (mttm) REVERT: M 34 LYS cc_start: 0.8035 (mttt) cc_final: 0.7794 (mttt) REVERT: N 42 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8745 (p) outliers start: 52 outliers final: 42 residues processed: 207 average time/residue: 0.5224 time to fit residues: 113.5213 Evaluate side-chains 229 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR 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 44 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER 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 44 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 80 LYS 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 N residue 42 SER Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.109811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091435 restraints weight = 8776.557| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.22 r_work: 0.3328 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 7575 Z= 0.251 Angle : 0.623 6.453 10215 Z= 0.340 Chirality : 0.053 0.137 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.405 23.765 1080 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 6.41 % Allowed : 25.75 % Favored : 67.84 % 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: -2.18 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 39 PHE 0.020 0.004 PHE N 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 7575) covalent geometry : angle 0.62301 (10215) hydrogen bonds : bond 0.03518 ( 288) hydrogen bonds : angle 5.50759 ( 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 235 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.274 Fit side-chains REVERT: A 34 LYS cc_start: 0.8211 (mttt) cc_final: 0.7994 (mttt) REVERT: C 23 LYS cc_start: 0.7438 (tmtt) cc_final: 0.7190 (tptt) REVERT: E 35 GLU cc_start: 0.8119 (tt0) cc_final: 0.7434 (tm-30) REVERT: F 43 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8492 (ttmm) REVERT: F 61 GLU cc_start: 0.8182 (mp0) cc_final: 0.7456 (tt0) REVERT: G 15 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7793 (t) REVERT: H 35 GLU cc_start: 0.8092 (tt0) cc_final: 0.7397 (tm-30) REVERT: J 34 LYS cc_start: 0.8547 (mttt) cc_final: 0.8306 (mtpt) REVERT: J 35 GLU cc_start: 0.8151 (tt0) cc_final: 0.7524 (tm-30) REVERT: J 57 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: M 34 LYS cc_start: 0.8027 (mttt) cc_final: 0.7782 (mttt) REVERT: N 42 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8734 (p) outliers start: 49 outliers final: 43 residues processed: 207 average time/residue: 0.5524 time to fit residues: 119.9504 Evaluate side-chains 230 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR 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 44 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER 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 44 THR Chi-restraints excluded: chain L residue 44 THR 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 N residue 33 THR Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.0670 chunk 25 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 overall best weight: 6.6126 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.107076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089063 restraints weight = 9330.456| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.29 r_work: 0.3271 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 7575 Z= 0.340 Angle : 0.670 6.786 10215 Z= 0.368 Chirality : 0.055 0.136 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.592 24.921 1080 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 6.41 % Allowed : 26.54 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.29 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 39 PHE 0.021 0.005 PHE D 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00717 ( 7575) covalent geometry : angle 0.67036 (10215) hydrogen bonds : bond 0.03776 ( 288) hydrogen bonds : angle 5.51166 ( 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 240 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.202 Fit side-chains REVERT: C 23 LYS cc_start: 0.7512 (tmtt) cc_final: 0.7283 (tptt) REVERT: F 43 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8409 (tttm) REVERT: F 45 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8787 (tttp) REVERT: F 61 GLU cc_start: 0.8283 (mp0) cc_final: 0.7462 (tt0) REVERT: H 35 GLU cc_start: 0.8094 (tt0) cc_final: 0.7398 (tm-30) REVERT: J 34 LYS cc_start: 0.8523 (mttt) cc_final: 0.8264 (mtpt) REVERT: J 35 GLU cc_start: 0.8205 (tt0) cc_final: 0.7524 (tm-30) REVERT: L 46 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8138 (mt-10) REVERT: M 34 LYS cc_start: 0.8047 (mttt) cc_final: 0.7787 (mttt) REVERT: N 42 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8735 (p) outliers start: 49 outliers final: 42 residues processed: 212 average time/residue: 0.5458 time to fit residues: 121.4344 Evaluate side-chains 233 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR 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 44 THR Chi-restraints excluded: chain L residue 44 THR 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 N residue 42 SER Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 20.0000 chunk 102 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.113076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094890 restraints weight = 8646.698| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.21 r_work: 0.3386 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7575 Z= 0.179 Angle : 0.615 6.365 10215 Z= 0.329 Chirality : 0.052 0.132 1365 Planarity : 0.002 0.009 1245 Dihedral : 5.106 23.555 1080 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.36 % Allowed : 28.24 % Favored : 66.41 % 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: -2.29 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 39 PHE 0.019 0.004 PHE D 94 HIS 0.003 0.001 HIS N 50 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7575) covalent geometry : angle 0.61456 (10215) hydrogen bonds : bond 0.03207 ( 288) hydrogen bonds : angle 5.45396 ( 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 222 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.251 Fit side-chains REVERT: E 35 GLU cc_start: 0.8091 (tt0) cc_final: 0.7402 (tm-30) REVERT: F 43 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8382 (tttm) REVERT: F 61 GLU cc_start: 0.8085 (mp0) cc_final: 0.7356 (tt0) REVERT: G 15 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7764 (t) REVERT: H 35 GLU cc_start: 0.8053 (tt0) cc_final: 0.7393 (tm-30) REVERT: J 34 LYS cc_start: 0.8463 (mttt) cc_final: 0.8209 (mtpt) REVERT: J 35 GLU cc_start: 0.8156 (tt0) cc_final: 0.7528 (tm-30) REVERT: J 42 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8677 (p) REVERT: L 46 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8164 (mt-10) REVERT: M 34 LYS cc_start: 0.8012 (mttt) cc_final: 0.7765 (mttt) REVERT: O 45 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8244 (tppt) outliers start: 41 outliers final: 32 residues processed: 196 average time/residue: 0.5384 time to fit residues: 110.7467 Evaluate side-chains 211 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 44 THR 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 N residue 33 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.111014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.092759 restraints weight = 8910.629| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.23 r_work: 0.3276 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 7575 Z= 0.358 Angle : 0.707 6.721 10215 Z= 0.384 Chirality : 0.055 0.135 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.526 24.785 1080 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.58 % Allowed : 29.41 % 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: -2.38 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR L 39 PHE 0.021 0.005 PHE D 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00757 ( 7575) covalent geometry : angle 0.70687 (10215) hydrogen bonds : bond 0.03745 ( 288) hydrogen bonds : angle 5.48413 ( 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 223 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.237 Fit side-chains REVERT: F 43 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8372 (tttm) REVERT: F 45 LYS cc_start: 0.9073 (ttpt) cc_final: 0.8847 (tttp) REVERT: F 61 GLU cc_start: 0.8291 (mp0) cc_final: 0.7484 (tt0) REVERT: H 35 GLU cc_start: 0.8071 (tt0) cc_final: 0.7406 (tm-30) REVERT: J 34 LYS cc_start: 0.8562 (mttt) cc_final: 0.8303 (mtpt) REVERT: J 35 GLU cc_start: 0.8209 (tt0) cc_final: 0.7563 (tm-30) REVERT: L 46 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8252 (mt-10) REVERT: M 34 LYS cc_start: 0.8052 (mttt) cc_final: 0.7794 (mttt) outliers start: 35 outliers final: 32 residues processed: 200 average time/residue: 0.5367 time to fit residues: 112.6146 Evaluate side-chains 219 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.113075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094976 restraints weight = 8853.711| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.23 r_work: 0.3344 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7575 Z= 0.253 Angle : 0.668 6.877 10215 Z= 0.358 Chirality : 0.053 0.134 1365 Planarity : 0.002 0.009 1245 Dihedral : 5.299 23.793 1080 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.71 % Allowed : 29.54 % 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: -2.40 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 39 PHE 0.019 0.004 PHE D 94 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 7575) covalent geometry : angle 0.66834 (10215) hydrogen bonds : bond 0.03440 ( 288) hydrogen bonds : angle 5.45139 ( 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 221 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.234 Fit side-chains REVERT: E 35 GLU cc_start: 0.8177 (tt0) cc_final: 0.7427 (tm-30) REVERT: F 34 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8129 (mtmt) REVERT: F 43 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8378 (tttm) REVERT: F 45 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8833 (tttp) REVERT: F 61 GLU cc_start: 0.8290 (mp0) cc_final: 0.7499 (tt0) REVERT: H 35 GLU cc_start: 0.8037 (tt0) cc_final: 0.7395 (tm-30) REVERT: J 34 LYS cc_start: 0.8544 (mttt) cc_final: 0.8285 (mtpt) REVERT: J 35 GLU cc_start: 0.8205 (tt0) cc_final: 0.7557 (tm-30) REVERT: J 57 GLU cc_start: 0.8871 (tt0) cc_final: 0.8550 (tt0) REVERT: L 46 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8272 (mt-10) REVERT: M 34 LYS cc_start: 0.8063 (mttt) cc_final: 0.7806 (mttt) REVERT: O 45 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8256 (tppt) outliers start: 36 outliers final: 36 residues processed: 196 average time/residue: 0.5002 time to fit residues: 103.0257 Evaluate side-chains 221 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 44 THR 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 N residue 44 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.109009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.090802 restraints weight = 9087.347| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.24 r_work: 0.3256 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.043 7575 Z= 0.426 Angle : 0.749 7.027 10215 Z= 0.410 Chirality : 0.057 0.145 1365 Planarity : 0.002 0.010 1245 Dihedral : 5.655 25.190 1080 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.23 % Allowed : 29.02 % 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: -2.44 (0.21), residues: 1035 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 39 PHE 0.021 0.005 PHE I 94 HIS 0.004 0.002 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00904 ( 7575) covalent geometry : angle 0.74878 (10215) hydrogen bonds : bond 0.03939 ( 288) hydrogen bonds : angle 5.50703 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2735.87 seconds wall clock time: 47 minutes 19.50 seconds (2839.50 seconds total)