Starting phenix.real_space_refine on Tue Feb 3 16:36:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hcb_52043/02_2026/9hcb_52043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hcb_52043/02_2026/9hcb_52043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hcb_52043/02_2026/9hcb_52043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hcb_52043/02_2026/9hcb_52043.map" model { file = "/net/cci-nas-00/data/ceres_data/9hcb_52043/02_2026/9hcb_52043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hcb_52043/02_2026/9hcb_52043.cif" } resolution = 2.95 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= 0.001 sd= 0.011 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 3160 2.51 5 N 870 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5040 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" 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 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 Chain: "B" 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 Chain: "D" 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 Chain: "E" 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 Chain: "F" 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 Chain: "G" 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 Chain: "H" 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 Chain: "I" 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 Chain: "J" 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 Time building chain proxies: 1.21, per 1000 atoms: 0.24 Number of scatterers: 5040 At special positions: 0 Unit cell: (147, 90.3, 48.3, 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 1010 8.00 N 870 7.00 C 3160 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: 0.33 Conformation dependent library (CDL) restraints added in 376.0 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 57.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.495A pdb=" N VAL A 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA B 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU A 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 16 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA D 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 18 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS D 21 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU C 20 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.173A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS C 34 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS D 34 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 49 removed outlier: 6.353A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU B 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS A 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N VAL B 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU C 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY B 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU D 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU E 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LYS D 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N VAL E 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 57 removed outlier: 6.340A pdb=" N VAL C 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR C 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLU B 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA C 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.711A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU C 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N THR D 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL D 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN C 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 70 through 79 removed outlier: 6.788A pdb=" N VAL B 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR A 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY B 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N VAL C 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N VAL B 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLY C 73 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 76 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA B 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 71 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR C 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY D 73 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL E 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR D 72 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY E 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.515A 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 91 removed outlier: 6.418A pdb=" N GLY D 86 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ALA E 89 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ALA E 91 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA D 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 16 through 22 removed outlier: 6.689A pdb=" N VAL F 16 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA G 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA F 18 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LYS G 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU F 20 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL G 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA H 19 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU G 20 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL H 16 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA I 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA H 18 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LYS I 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU H 20 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL I 16 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA J 19 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA I 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS J 21 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 6.348A 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: 6.160A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 6.100A 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: 6.665A pdb=" N TYR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N SER G 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY F 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR G 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU G 46 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LYS F 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL G 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER I 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU I 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER J 42 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY I 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N THR J 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU J 46 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS I 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N VAL J 48 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 8.984A 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 removed outlier: 6.799A pdb=" N GLU F 61 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N THR G 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL F 63 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL G 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN F 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU G 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N THR H 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL G 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL H 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN G 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU H 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N THR I 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL H 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL I 66 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASN H 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU I 61 " --> pdb=" O GLN J 62 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N THR J 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL J 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN I 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 70 through 79 removed outlier: 6.865A pdb=" N VAL G 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR F 72 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY G 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL F 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL H 71 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR G 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY H 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL G 74 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL I 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR H 72 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY I 73 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL H 74 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL J 71 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR I 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY J 73 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 6.506A 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 91 removed outlier: 6.445A pdb=" N GLY F 86 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA G 89 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE F 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA G 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY H 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA I 89 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE H 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA I 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA H 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 880 1.27 - 1.34: 760 1.34 - 1.41: 170 1.41 - 1.48: 878 1.48 - 1.55: 2362 Bond restraints: 5050 Sorted by residual: bond pdb=" CA SER D 87 " pdb=" C SER D 87 " ideal model delta sigma weight residual 1.520 1.477 0.043 1.16e-02 7.43e+03 1.40e+01 bond pdb=" CA SER G 87 " pdb=" C SER G 87 " ideal model delta sigma weight residual 1.520 1.477 0.043 1.16e-02 7.43e+03 1.38e+01 bond pdb=" CA SER H 87 " pdb=" C SER H 87 " ideal model delta sigma weight residual 1.520 1.477 0.043 1.16e-02 7.43e+03 1.37e+01 bond pdb=" CA SER C 87 " pdb=" C SER C 87 " ideal model delta sigma weight residual 1.520 1.477 0.043 1.16e-02 7.43e+03 1.36e+01 bond pdb=" CA SER B 87 " pdb=" C SER B 87 " ideal model delta sigma weight residual 1.520 1.477 0.043 1.16e-02 7.43e+03 1.35e+01 ... (remaining 5045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 5622 2.62 - 5.24: 988 5.24 - 7.86: 110 7.86 - 10.48: 80 10.48 - 13.10: 10 Bond angle restraints: 6810 Sorted by residual: angle pdb=" N VAL G 74 " pdb=" CA VAL G 74 " pdb=" C VAL G 74 " ideal model delta sigma weight residual 110.62 100.22 10.40 1.02e+00 9.61e-01 1.04e+02 angle pdb=" N VAL F 74 " pdb=" CA VAL F 74 " pdb=" C VAL F 74 " ideal model delta sigma weight residual 110.62 100.23 10.39 1.02e+00 9.61e-01 1.04e+02 angle pdb=" N VAL I 74 " pdb=" CA VAL I 74 " pdb=" C VAL I 74 " ideal model delta sigma weight residual 110.62 100.24 10.38 1.02e+00 9.61e-01 1.04e+02 angle pdb=" N VAL D 74 " pdb=" CA VAL D 74 " pdb=" C VAL D 74 " ideal model delta sigma weight residual 110.62 100.25 10.37 1.02e+00 9.61e-01 1.03e+02 angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 110.62 100.25 10.37 1.02e+00 9.61e-01 1.03e+02 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 2560 14.59 - 29.18: 270 29.18 - 43.78: 120 43.78 - 58.37: 10 58.37 - 72.96: 20 Dihedral angle restraints: 2980 sinusoidal: 1000 harmonic: 1980 Sorted by residual: 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 -131.27 8.67 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C HIS F 50 " pdb=" N HIS F 50 " pdb=" CA HIS F 50 " pdb=" CB HIS F 50 " ideal model delta harmonic sigma weight residual -122.60 -131.22 8.62 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" C HIS C 50 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " pdb=" CB HIS C 50 " ideal model delta harmonic sigma weight residual -122.60 -131.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 623 0.088 - 0.177: 202 0.177 - 0.265: 75 0.265 - 0.353: 0 0.353 - 0.442: 10 Chirality restraints: 910 Sorted by residual: 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 2.07 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CA HIS A 50 " pdb=" N HIS A 50 " pdb=" C HIS A 50 " pdb=" CB HIS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA HIS F 50 " pdb=" N HIS F 50 " pdb=" C HIS F 50 " pdb=" CB HIS F 50 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 907 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 92 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C THR B 92 " -0.041 2.00e-02 2.50e+03 pdb=" O THR B 92 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 93 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 92 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C THR F 92 " 0.040 2.00e-02 2.50e+03 pdb=" O THR F 92 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY F 93 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 92 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C THR C 92 " -0.040 2.00e-02 2.50e+03 pdb=" O THR C 92 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY C 93 " 0.014 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 2253 2.91 - 3.41: 4232 3.41 - 3.91: 9321 3.91 - 4.40: 10127 4.40 - 4.90: 18680 Nonbonded interactions: 44613 Sorted by model distance: nonbonded pdb=" N GLU H 83 " pdb=" O GLU H 83 " model vdw 2.414 2.496 nonbonded pdb=" N GLU J 83 " pdb=" O GLU J 83 " model vdw 2.414 2.496 nonbonded pdb=" N GLU B 83 " pdb=" O GLU B 83 " model vdw 2.414 2.496 nonbonded pdb=" N GLU A 83 " pdb=" O GLU A 83 " model vdw 2.414 2.496 nonbonded pdb=" N GLU G 83 " pdb=" O GLU G 83 " model vdw 2.414 2.496 ... (remaining 44608 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 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.700 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 5050 Z= 1.186 Angle : 2.214 13.095 6810 Z= 1.544 Chirality : 0.102 0.442 910 Planarity : 0.005 0.023 830 Dihedral : 15.920 72.961 1720 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.92 % Allowed : 18.24 % Favored : 77.84 % 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: 0.55 (0.33), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.43 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR B 39 PHE 0.020 0.007 PHE I 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.01536 ( 5050) covalent geometry : angle 2.21364 ( 6810) hydrogen bonds : bond 0.08599 ( 120) hydrogen bonds : angle 8.05656 ( 360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.205 Fit side-chains REVERT: C 46 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7041 (tm-30) REVERT: A 46 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7410 (tm-30) REVERT: D 15 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6936 (t) REVERT: D 80 LYS cc_start: 0.8723 (mttm) cc_final: 0.8465 (mttp) REVERT: D 83 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7492 (mt-10) REVERT: G 23 LYS cc_start: 0.7507 (tmtt) cc_final: 0.7115 (tmtt) REVERT: I 57 GLU cc_start: 0.7939 (tt0) cc_final: 0.7738 (tt0) outliers start: 20 outliers final: 13 residues processed: 123 average time/residue: 0.4392 time to fit residues: 56.3787 Evaluate side-chains 103 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain J residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.133489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.115419 restraints weight = 5722.846| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.41 r_work: 0.3774 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5050 Z= 0.141 Angle : 0.543 7.067 6810 Z= 0.299 Chirality : 0.052 0.133 910 Planarity : 0.002 0.010 830 Dihedral : 6.535 34.208 734 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 24.90 % Favored : 71.18 % 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: -0.94 (0.29), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR H 39 PHE 0.011 0.002 PHE E 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5050) covalent geometry : angle 0.54302 ( 6810) hydrogen bonds : bond 0.02382 ( 120) hydrogen bonds : angle 5.41991 ( 360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.121 Fit side-chains REVERT: A 20 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7065 (tm-30) REVERT: A 94 PHE cc_start: 0.8039 (p90) cc_final: 0.4728 (t80) REVERT: F 65 ASN cc_start: 0.9032 (t0) cc_final: 0.8829 (t0) REVERT: H 23 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.7132 (tptp) REVERT: I 23 LYS cc_start: 0.7113 (tmtt) cc_final: 0.6824 (tmtt) REVERT: J 75 THR cc_start: 0.8847 (m) cc_final: 0.8621 (t) REVERT: J 79 GLN cc_start: 0.8890 (tt0) cc_final: 0.8609 (tt0) outliers start: 20 outliers final: 12 residues processed: 92 average time/residue: 0.4653 time to fit residues: 44.4948 Evaluate side-chains 83 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.112684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094887 restraints weight = 6197.224| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.31 r_work: 0.3458 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.052 5050 Z= 0.547 Angle : 0.806 10.536 6810 Z= 0.443 Chirality : 0.060 0.178 910 Planarity : 0.003 0.013 830 Dihedral : 6.849 23.022 722 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.08 % Allowed : 22.75 % Favored : 71.18 % 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: -1.83 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.022 0.005 PHE B 94 HIS 0.008 0.003 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.01152 ( 5050) covalent geometry : angle 0.80581 ( 6810) hydrogen bonds : bond 0.03302 ( 120) hydrogen bonds : angle 5.04097 ( 360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.119 Fit side-chains REVERT: B 59 THR cc_start: 0.8789 (m) cc_final: 0.8586 (m) REVERT: F 21 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7007 (mttt) REVERT: F 46 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: H 23 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7119 (tttm) REVERT: J 23 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6853 (ttpt) REVERT: J 79 GLN cc_start: 0.9046 (tt0) cc_final: 0.8702 (tt0) outliers start: 31 outliers final: 25 residues processed: 84 average time/residue: 0.3153 time to fit residues: 27.9032 Evaluate side-chains 88 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 LYS 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 75 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 23 LYS 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 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.127022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.109402 restraints weight = 5836.588| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.38 r_work: 0.3667 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5050 Z= 0.128 Angle : 0.519 7.707 6810 Z= 0.281 Chirality : 0.051 0.125 910 Planarity : 0.002 0.009 830 Dihedral : 5.467 21.322 721 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.31 % Allowed : 25.29 % Favored : 70.39 % 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: -1.82 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR H 39 PHE 0.013 0.002 PHE C 94 HIS 0.001 0.000 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5050) covalent geometry : angle 0.51936 ( 6810) hydrogen bonds : bond 0.02083 ( 120) hydrogen bonds : angle 4.42210 ( 360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.142 Fit side-chains REVERT: A 20 GLU cc_start: 0.7332 (tm-30) cc_final: 0.7079 (tm-30) REVERT: H 23 LYS cc_start: 0.7207 (ttpt) cc_final: 0.6995 (tptp) REVERT: J 79 GLN cc_start: 0.9037 (tt0) cc_final: 0.8557 (tt0) outliers start: 22 outliers final: 18 residues processed: 79 average time/residue: 0.3461 time to fit residues: 28.7361 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.112829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095446 restraints weight = 6631.272| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.40 r_work: 0.3488 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 5050 Z= 0.355 Angle : 0.651 10.346 6810 Z= 0.352 Chirality : 0.054 0.140 910 Planarity : 0.002 0.010 830 Dihedral : 6.022 20.452 720 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 6.67 % Allowed : 22.55 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.019 0.004 PHE C 94 HIS 0.005 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00734 ( 5050) covalent geometry : angle 0.65100 ( 6810) hydrogen bonds : bond 0.02617 ( 120) hydrogen bonds : angle 4.72190 ( 360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.233 Fit side-chains REVERT: C 61 GLU cc_start: 0.6945 (mp0) cc_final: 0.6499 (mp0) REVERT: A 20 GLU cc_start: 0.7275 (tm-30) cc_final: 0.7067 (tm-30) outliers start: 34 outliers final: 29 residues processed: 87 average time/residue: 0.3909 time to fit residues: 35.7874 Evaluate side-chains 91 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 0.0060 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.112884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.094380 restraints weight = 7001.235| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.67 r_work: 0.3545 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5050 Z= 0.173 Angle : 0.551 8.691 6810 Z= 0.294 Chirality : 0.051 0.126 910 Planarity : 0.002 0.009 830 Dihedral : 5.383 19.275 720 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 5.10 % Allowed : 24.51 % Favored : 70.39 % 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: -2.21 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR J 39 PHE 0.015 0.002 PHE C 94 HIS 0.002 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5050) covalent geometry : angle 0.55051 ( 6810) hydrogen bonds : bond 0.02032 ( 120) hydrogen bonds : angle 4.34885 ( 360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.187 Fit side-chains REVERT: A 20 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6971 (tm-30) REVERT: F 46 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: J 79 GLN cc_start: 0.9002 (tt0) cc_final: 0.8594 (tt0) outliers start: 26 outliers final: 24 residues processed: 84 average time/residue: 0.3794 time to fit residues: 33.6315 Evaluate side-chains 88 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 15 VAL 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 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.106744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087828 restraints weight = 7059.310| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.68 r_work: 0.3432 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 5050 Z= 0.352 Angle : 0.669 10.361 6810 Z= 0.356 Chirality : 0.054 0.137 910 Planarity : 0.002 0.010 830 Dihedral : 5.858 20.113 720 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 6.08 % Allowed : 24.51 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 39 PHE 0.020 0.004 PHE C 94 HIS 0.005 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00731 ( 5050) covalent geometry : angle 0.66873 ( 6810) hydrogen bonds : bond 0.02472 ( 120) hydrogen bonds : angle 4.55779 ( 360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.199 Fit side-chains REVERT: A 20 GLU cc_start: 0.7243 (tm-30) cc_final: 0.7009 (tm-30) REVERT: E 61 GLU cc_start: 0.7559 (mp0) cc_final: 0.7118 (mp0) REVERT: F 46 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8217 (tt0) outliers start: 31 outliers final: 28 residues processed: 86 average time/residue: 0.4171 time to fit residues: 37.6666 Evaluate side-chains 94 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 33 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 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 59 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.110969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.092828 restraints weight = 7103.938| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.66 r_work: 0.3553 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5050 Z= 0.171 Angle : 0.576 9.246 6810 Z= 0.301 Chirality : 0.052 0.125 910 Planarity : 0.002 0.008 830 Dihedral : 5.252 19.257 720 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.90 % Allowed : 25.69 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR J 39 PHE 0.016 0.002 PHE C 94 HIS 0.002 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5050) covalent geometry : angle 0.57558 ( 6810) hydrogen bonds : bond 0.01950 ( 120) hydrogen bonds : angle 4.17652 ( 360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.115 Fit side-chains REVERT: A 20 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6872 (tm-30) REVERT: F 46 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: J 79 GLN cc_start: 0.8982 (tt0) cc_final: 0.8713 (tt0) outliers start: 25 outliers final: 24 residues processed: 80 average time/residue: 0.4277 time to fit residues: 35.7930 Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 33 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 46 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.105743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.087346 restraints weight = 7158.434| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.61 r_work: 0.3454 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 5050 Z= 0.360 Angle : 0.691 9.770 6810 Z= 0.366 Chirality : 0.055 0.138 910 Planarity : 0.002 0.009 830 Dihedral : 5.803 19.839 720 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.29 % Allowed : 25.88 % Favored : 68.82 % 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: -2.58 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR D 39 PHE 0.020 0.004 PHE C 94 HIS 0.005 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00750 ( 5050) covalent geometry : angle 0.69084 ( 6810) hydrogen bonds : bond 0.02443 ( 120) hydrogen bonds : angle 4.50771 ( 360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.193 Fit side-chains REVERT: E 61 GLU cc_start: 0.7556 (mp0) cc_final: 0.7132 (mp0) REVERT: F 46 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8191 (tt0) outliers start: 27 outliers final: 25 residues processed: 85 average time/residue: 0.4475 time to fit residues: 39.8902 Evaluate side-chains 92 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 33 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 46 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 42 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.112620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.094661 restraints weight = 6958.760| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.63 r_work: 0.3586 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5050 Z= 0.149 Angle : 0.588 8.979 6810 Z= 0.306 Chirality : 0.052 0.123 910 Planarity : 0.002 0.008 830 Dihedral : 5.134 18.824 720 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.51 % Allowed : 28.04 % Favored : 67.45 % 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: -2.47 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR H 39 PHE 0.015 0.002 PHE C 94 HIS 0.001 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5050) covalent geometry : angle 0.58801 ( 6810) hydrogen bonds : bond 0.01793 ( 120) hydrogen bonds : angle 4.08316 ( 360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.161 Fit side-chains REVERT: G 80 LYS cc_start: 0.8892 (mttp) cc_final: 0.8619 (ttmt) REVERT: J 79 GLN cc_start: 0.8973 (tt0) cc_final: 0.8577 (tt0) outliers start: 23 outliers final: 22 residues processed: 79 average time/residue: 0.5120 time to fit residues: 42.3014 Evaluate side-chains 87 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 33 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 G residue 15 VAL Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 67 optimal weight: 0.0670 chunk 62 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 overall best weight: 2.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN G 79 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.110375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.092056 restraints weight = 7103.824| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.66 r_work: 0.3502 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5050 Z= 0.189 Angle : 0.600 9.012 6810 Z= 0.311 Chirality : 0.052 0.127 910 Planarity : 0.002 0.008 830 Dihedral : 5.209 18.762 720 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.71 % Allowed : 27.45 % 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: -2.47 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 39 PHE 0.015 0.002 PHE C 94 HIS 0.002 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5050) covalent geometry : angle 0.59962 ( 6810) hydrogen bonds : bond 0.01914 ( 120) hydrogen bonds : angle 4.08543 ( 360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1506.66 seconds wall clock time: 26 minutes 43.80 seconds (1603.80 seconds total)