Starting phenix.real_space_refine on Tue Feb 3 14:23:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y0s_72396/02_2026/9y0s_72396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y0s_72396/02_2026/9y0s_72396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y0s_72396/02_2026/9y0s_72396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y0s_72396/02_2026/9y0s_72396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y0s_72396/02_2026/9y0s_72396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y0s_72396/02_2026/9y0s_72396.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 2260 2.51 5 N 640 2.21 5 O 750 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: 3650 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 365 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.55, per 1000 atoms: 0.15 Number of scatterers: 3650 At special positions: 0 Unit cell: (93, 80.91, 41.85, 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 750 8.00 N 640 7.00 C 2260 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: 0.36 Conformation dependent library (CDL) restraints added in 190.1 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 55.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 45 through 56 removed outlier: 6.727A pdb=" N VAL D 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL H 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS D 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY H 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL D 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N HIS A 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY D 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS A 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL E 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLY A 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N HIS E 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N VAL A 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL E 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY A 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR E 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA A 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ALA E 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS E 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL I 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLY E 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N HIS I 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N VAL E 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N VAL I 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY E 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR I 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA E 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA I 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL E 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 60 through 66 removed outlier: 6.432A pdb=" N LYS A 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL E 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN A 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASN E 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR A 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS E 60 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL I 63 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN E 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASN I 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR E 64 " --> pdb=" O ASN I 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 70 through 78 removed outlier: 7.000A pdb=" N VAL D 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR H 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY D 73 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL D 77 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA H 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR D 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA D 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N GLY E 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR A 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR E 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL E 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ALA A 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N VAL E 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N GLY I 73 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR E 72 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR I 75 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL E 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL I 77 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA E 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.962A pdb=" N GLU H 83 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU D 83 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N THR E 81 " --> pdb=" O VAL I 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 86 through 88 removed outlier: 6.648A pdb=" N SER D 87 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER A 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 91 through 92 removed outlier: 6.201A pdb=" N ALA A 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA E 91 " --> pdb=" O THR I 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 45 through 56 removed outlier: 6.741A pdb=" N VAL B 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL F 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS B 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY F 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N HIS C 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR C 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA C 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS C 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL G 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY C 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N HIS G 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL C 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N VAL G 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY C 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR G 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA C 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ALA G 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL C 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS G 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL J 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLY G 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N HIS J 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL G 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N VAL J 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY G 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR J 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA G 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ALA J 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL G 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 66 removed outlier: 6.421A pdb=" N LYS B 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL C 63 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN C 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR B 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS C 60 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL G 63 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN C 62 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN G 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 64 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS G 60 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL J 63 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN G 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASN J 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR G 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 70 through 78 removed outlier: 7.002A pdb=" N VAL B 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR F 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY B 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA F 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N GLY C 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N THR B 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR C 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL C 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N VAL C 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLY G 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR C 72 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N THR G 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 74 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL G 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA C 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N VAL G 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N GLY J 73 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N THR G 72 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N THR J 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL G 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL J 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA G 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 81 through 83 removed outlier: 6.992A pdb=" N GLU F 83 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR B 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N THR C 81 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N THR G 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 86 through 88 removed outlier: 6.635A pdb=" N SER B 87 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 92 removed outlier: 6.199A pdb=" N ALA B 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA C 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA G 91 " --> pdb=" O THR J 92 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 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: 0.52 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: 1.23 - 1.29: 650 1.29 - 1.36: 590 1.36 - 1.42: 100 1.42 - 1.49: 669 1.49 - 1.55: 1651 Bond restraints: 3660 Sorted by residual: bond pdb=" CB VAL F 95 " pdb=" CG2 VAL F 95 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB VAL E 95 " pdb=" CG2 VAL E 95 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.09e+00 bond pdb=" CB VAL H 95 " pdb=" CG2 VAL H 95 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB VAL D 95 " pdb=" CG2 VAL D 95 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB VAL G 95 " pdb=" CG2 VAL G 95 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 ... (remaining 3655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 4732 1.14 - 2.27: 148 2.27 - 3.41: 70 3.41 - 4.54: 0 4.54 - 5.68: 10 Bond angle restraints: 4960 Sorted by residual: angle pdb=" CB LYS I 80 " pdb=" CG LYS I 80 " pdb=" CD LYS I 80 " ideal model delta sigma weight residual 111.30 116.98 -5.68 2.30e+00 1.89e-01 6.09e+00 angle pdb=" CB LYS D 80 " pdb=" CG LYS D 80 " pdb=" CD LYS D 80 " ideal model delta sigma weight residual 111.30 116.98 -5.68 2.30e+00 1.89e-01 6.09e+00 angle pdb=" CB LYS G 80 " pdb=" CG LYS G 80 " pdb=" CD LYS G 80 " ideal model delta sigma weight residual 111.30 116.97 -5.67 2.30e+00 1.89e-01 6.08e+00 angle pdb=" CB LYS B 80 " pdb=" CG LYS B 80 " pdb=" CD LYS B 80 " ideal model delta sigma weight residual 111.30 116.96 -5.66 2.30e+00 1.89e-01 6.06e+00 angle pdb=" CB LYS E 80 " pdb=" CG LYS E 80 " pdb=" CD LYS E 80 " ideal model delta sigma weight residual 111.30 116.95 -5.65 2.30e+00 1.89e-01 6.04e+00 ... (remaining 4955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 1930 15.63 - 31.25: 130 31.25 - 46.88: 20 46.88 - 62.50: 20 62.50 - 78.12: 30 Dihedral angle restraints: 2130 sinusoidal: 680 harmonic: 1450 Sorted by residual: dihedral pdb=" CA PHE C 94 " pdb=" C PHE C 94 " pdb=" N VAL C 95 " pdb=" CA VAL C 95 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" CA PHE E 94 " pdb=" C PHE E 94 " pdb=" N VAL E 95 " pdb=" CA VAL E 95 " ideal model delta harmonic sigma weight residual 180.00 164.51 15.49 0 5.00e+00 4.00e-02 9.60e+00 dihedral pdb=" CA PHE G 94 " pdb=" C PHE G 94 " pdb=" N VAL G 95 " pdb=" CA VAL G 95 " ideal model delta harmonic sigma weight residual 180.00 164.53 15.47 0 5.00e+00 4.00e-02 9.58e+00 ... (remaining 2127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 408 0.037 - 0.075: 122 0.075 - 0.112: 115 0.112 - 0.149: 15 0.149 - 0.187: 10 Chirality restraints: 670 Sorted by residual: chirality pdb=" CB VAL I 95 " pdb=" CA VAL I 95 " pdb=" CG1 VAL I 95 " pdb=" CG2 VAL I 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CB VAL H 95 " pdb=" CA VAL H 95 " pdb=" CG1 VAL H 95 " pdb=" CG2 VAL H 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CB VAL D 95 " pdb=" CA VAL D 95 " pdb=" CG1 VAL D 95 " pdb=" CG2 VAL D 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 667 not shown) Planarity restraints: 620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 94 " -0.008 2.00e-02 2.50e+03 7.13e-03 8.89e-01 pdb=" CG PHE I 94 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE I 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE I 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE I 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE I 94 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.008 2.00e-02 2.50e+03 7.11e-03 8.86e-01 pdb=" CG PHE F 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.008 2.00e-02 2.50e+03 7.06e-03 8.73e-01 pdb=" CG PHE C 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.001 2.00e-02 2.50e+03 ... (remaining 617 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 2615 3.11 - 3.55: 3741 3.55 - 4.00: 5579 4.00 - 4.45: 6123 4.45 - 4.90: 12354 Nonbonded interactions: 30412 Sorted by model distance: nonbonded pdb=" OE1 GLN A 79 " pdb=" NE2 GLN D 79 " model vdw 2.657 3.120 nonbonded pdb=" NE2 GLN C 79 " pdb=" OE1 GLN G 79 " model vdw 2.666 3.120 nonbonded pdb=" NE2 GLN A 79 " pdb=" OE1 GLN E 79 " model vdw 2.673 3.120 nonbonded pdb=" NE2 GLN B 79 " pdb=" OE1 GLN C 79 " model vdw 2.674 3.120 nonbonded pdb=" N GLN B 79 " pdb=" O GLN B 79 " model vdw 2.676 2.496 ... (remaining 30407 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' } 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: 4.800 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: 0.020 Process input model: 5.870 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.003 0.035 3660 Z= 0.137 Angle : 0.612 5.676 4960 Z= 0.336 Chirality : 0.057 0.187 670 Planarity : 0.001 0.007 620 Dihedral : 16.915 78.125 1210 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % 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: -2.43 (0.28), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.21), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.005 PHE I 94 HIS 0.003 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3660) covalent geometry : angle 0.61210 ( 4960) hydrogen bonds : bond 0.12464 ( 64) hydrogen bonds : angle 7.00525 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.135 Fit side-chains REVERT: B 60 LYS cc_start: 0.7810 (tttm) cc_final: 0.7550 (mttt) REVERT: B 87 SER cc_start: 0.8851 (m) cc_final: 0.8629 (t) REVERT: C 60 LYS cc_start: 0.7747 (tttm) cc_final: 0.7476 (mttm) REVERT: C 87 SER cc_start: 0.8814 (m) cc_final: 0.8599 (p) REVERT: D 60 LYS cc_start: 0.7911 (tttm) cc_final: 0.7489 (mtpt) REVERT: E 60 LYS cc_start: 0.7767 (tttm) cc_final: 0.7499 (mttt) REVERT: F 60 LYS cc_start: 0.7889 (tttm) cc_final: 0.7550 (mtpt) REVERT: G 60 LYS cc_start: 0.7916 (tttm) cc_final: 0.7681 (mtpt) REVERT: H 60 LYS cc_start: 0.7962 (tttm) cc_final: 0.7668 (mttt) REVERT: H 82 VAL cc_start: 0.7812 (t) cc_final: 0.7584 (p) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.4056 time to fit residues: 31.0877 Evaluate side-chains 64 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 79 GLN F 79 GLN G 79 GLN H 62 GLN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.152756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.132702 restraints weight = 4520.745| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.47 r_work: 0.3923 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 3660 Z= 0.297 Angle : 0.697 4.475 4960 Z= 0.393 Chirality : 0.055 0.147 670 Planarity : 0.003 0.011 620 Dihedral : 5.982 17.060 530 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.97 % Allowed : 12.70 % Favored : 84.32 % 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: -2.33 (0.30), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.005 PHE A 94 HIS 0.006 0.003 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 3660) covalent geometry : angle 0.69655 ( 4960) hydrogen bonds : bond 0.02656 ( 64) hydrogen bonds : angle 5.41253 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.083 Fit side-chains REVERT: A 60 LYS cc_start: 0.7982 (tttm) cc_final: 0.7573 (mtpt) REVERT: B 60 LYS cc_start: 0.8078 (tttm) cc_final: 0.7678 (mttt) REVERT: C 60 LYS cc_start: 0.8029 (tttm) cc_final: 0.7476 (mttm) REVERT: D 60 LYS cc_start: 0.8017 (tttm) cc_final: 0.7435 (mttt) REVERT: D 62 GLN cc_start: 0.7787 (tt0) cc_final: 0.7382 (tm-30) REVERT: E 60 LYS cc_start: 0.8080 (tttm) cc_final: 0.7631 (mttt) REVERT: E 92 THR cc_start: 0.7549 (p) cc_final: 0.7196 (m) REVERT: F 60 LYS cc_start: 0.7887 (tttm) cc_final: 0.7416 (mtpt) REVERT: G 60 LYS cc_start: 0.8068 (tttm) cc_final: 0.7666 (mttt) REVERT: H 60 LYS cc_start: 0.8022 (tttm) cc_final: 0.7521 (mttt) REVERT: I 61 GLU cc_start: 0.8102 (tt0) cc_final: 0.7669 (mt-10) REVERT: J 92 THR cc_start: 0.7415 (p) cc_final: 0.7135 (t) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.3676 time to fit residues: 34.3871 Evaluate side-chains 87 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN E 62 GLN E 79 GLN F 79 GLN H 62 GLN I 79 GLN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.157419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.137781 restraints weight = 4356.504| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.47 r_work: 0.3979 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3660 Z= 0.135 Angle : 0.502 3.404 4960 Z= 0.286 Chirality : 0.051 0.135 670 Planarity : 0.002 0.006 620 Dihedral : 4.975 13.840 530 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.16 % Allowed : 17.30 % Favored : 80.54 % 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: -2.57 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE B 94 HIS 0.005 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3660) covalent geometry : angle 0.50206 ( 4960) hydrogen bonds : bond 0.01743 ( 64) hydrogen bonds : angle 4.74982 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.089 Fit side-chains REVERT: A 60 LYS cc_start: 0.7998 (tttm) cc_final: 0.7585 (mtpt) REVERT: B 60 LYS cc_start: 0.8026 (tttm) cc_final: 0.7660 (mttt) REVERT: B 87 SER cc_start: 0.8829 (m) cc_final: 0.8547 (t) REVERT: C 60 LYS cc_start: 0.8059 (tttm) cc_final: 0.7551 (mttm) REVERT: D 60 LYS cc_start: 0.7997 (tttm) cc_final: 0.7434 (mttt) REVERT: D 62 GLN cc_start: 0.7768 (tt0) cc_final: 0.7402 (tm-30) REVERT: E 60 LYS cc_start: 0.8061 (tttm) cc_final: 0.7656 (mttt) REVERT: F 60 LYS cc_start: 0.7885 (tttm) cc_final: 0.7435 (mtpt) REVERT: G 60 LYS cc_start: 0.8008 (tttm) cc_final: 0.7629 (mtpt) REVERT: H 60 LYS cc_start: 0.8058 (tttm) cc_final: 0.7555 (mttt) REVERT: J 46 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5633 (tt0) outliers start: 8 outliers final: 4 residues processed: 88 average time/residue: 0.3973 time to fit residues: 36.1390 Evaluate side-chains 81 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 79 GLN F 79 GLN H 62 GLN I 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.154985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.134675 restraints weight = 4338.833| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.48 r_work: 0.3932 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3660 Z= 0.193 Angle : 0.562 3.851 4960 Z= 0.319 Chirality : 0.052 0.136 670 Planarity : 0.002 0.008 620 Dihedral : 5.311 16.131 530 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.59 % Allowed : 15.95 % Favored : 79.46 % 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: -2.60 (0.30), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE B 94 HIS 0.007 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 3660) covalent geometry : angle 0.56173 ( 4960) hydrogen bonds : bond 0.01857 ( 64) hydrogen bonds : angle 4.69151 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.084 Fit side-chains REVERT: A 60 LYS cc_start: 0.8000 (tttm) cc_final: 0.7570 (mtpt) REVERT: B 60 LYS cc_start: 0.8012 (tttm) cc_final: 0.7609 (mttt) REVERT: B 87 SER cc_start: 0.8810 (m) cc_final: 0.8516 (t) REVERT: C 60 LYS cc_start: 0.8005 (tttm) cc_final: 0.7497 (mttm) REVERT: D 60 LYS cc_start: 0.7993 (tttm) cc_final: 0.7389 (mttt) REVERT: D 62 GLN cc_start: 0.7793 (tt0) cc_final: 0.7374 (tm-30) REVERT: E 60 LYS cc_start: 0.8098 (tttm) cc_final: 0.7671 (mtpt) REVERT: F 60 LYS cc_start: 0.7896 (tttm) cc_final: 0.7386 (mtpt) REVERT: G 60 LYS cc_start: 0.8008 (tttm) cc_final: 0.7579 (mtpt) REVERT: G 92 THR cc_start: 0.7618 (p) cc_final: 0.7240 (t) REVERT: H 60 LYS cc_start: 0.8011 (tttm) cc_final: 0.7481 (mttt) REVERT: I 46 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6528 (mt-10) outliers start: 17 outliers final: 13 residues processed: 88 average time/residue: 0.3926 time to fit residues: 35.8741 Evaluate side-chains 89 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN F 79 GLN H 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.161123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.140838 restraints weight = 4336.586| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.48 r_work: 0.4004 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3660 Z= 0.107 Angle : 0.469 3.236 4960 Z= 0.267 Chirality : 0.050 0.131 670 Planarity : 0.001 0.007 620 Dihedral : 4.598 11.504 530 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.89 % Allowed : 20.54 % Favored : 77.57 % 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: -2.64 (0.29), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE I 94 HIS 0.005 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3660) covalent geometry : angle 0.46895 ( 4960) hydrogen bonds : bond 0.01451 ( 64) hydrogen bonds : angle 4.37145 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.083 Fit side-chains REVERT: A 60 LYS cc_start: 0.8017 (tttm) cc_final: 0.7575 (mtpt) REVERT: B 60 LYS cc_start: 0.7945 (tttm) cc_final: 0.7512 (mtpt) REVERT: B 87 SER cc_start: 0.8817 (m) cc_final: 0.8536 (t) REVERT: C 60 LYS cc_start: 0.8060 (tttm) cc_final: 0.7544 (mttm) REVERT: D 60 LYS cc_start: 0.7981 (tttm) cc_final: 0.7353 (mtpt) REVERT: D 62 GLN cc_start: 0.7786 (tt0) cc_final: 0.7414 (tm-30) REVERT: E 46 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7737 (mt-10) REVERT: E 60 LYS cc_start: 0.8066 (tttm) cc_final: 0.7634 (mttt) REVERT: F 60 LYS cc_start: 0.7851 (tttm) cc_final: 0.7360 (mtpt) REVERT: G 60 LYS cc_start: 0.8004 (tttm) cc_final: 0.7572 (mtmt) REVERT: H 60 LYS cc_start: 0.8009 (tttm) cc_final: 0.7469 (mttt) REVERT: I 46 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6461 (mt-10) REVERT: J 46 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6374 (tt0) outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 0.3217 time to fit residues: 26.6283 Evaluate side-chains 77 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 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 62 GLN F 79 GLN G 79 GLN H 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.153321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.132574 restraints weight = 4423.147| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.49 r_work: 0.3905 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 3660 Z= 0.253 Angle : 0.625 4.233 4960 Z= 0.353 Chirality : 0.053 0.139 670 Planarity : 0.002 0.010 620 Dihedral : 5.593 17.872 530 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 5.14 % Allowed : 18.38 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.30), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.004 PHE B 94 HIS 0.008 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 3660) covalent geometry : angle 0.62451 ( 4960) hydrogen bonds : bond 0.01984 ( 64) hydrogen bonds : angle 4.72257 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.167 Fit side-chains REVERT: A 60 LYS cc_start: 0.8003 (tttm) cc_final: 0.7546 (mttt) REVERT: B 60 LYS cc_start: 0.7945 (tttm) cc_final: 0.7494 (mttt) REVERT: B 87 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8514 (t) REVERT: C 60 LYS cc_start: 0.8007 (tttm) cc_final: 0.7520 (mttm) REVERT: D 60 LYS cc_start: 0.7991 (tttm) cc_final: 0.7343 (mttt) REVERT: D 62 GLN cc_start: 0.7800 (tt0) cc_final: 0.7343 (tm-30) REVERT: E 60 LYS cc_start: 0.8157 (tttm) cc_final: 0.7685 (mttt) REVERT: F 60 LYS cc_start: 0.7871 (tttm) cc_final: 0.7346 (mtpt) REVERT: G 60 LYS cc_start: 0.8040 (tttm) cc_final: 0.7587 (mtmt) REVERT: G 92 THR cc_start: 0.7609 (p) cc_final: 0.7244 (t) REVERT: H 60 LYS cc_start: 0.8032 (tttm) cc_final: 0.7478 (mttt) REVERT: I 46 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6404 (mt-10) REVERT: J 46 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6517 (tt0) outliers start: 19 outliers final: 13 residues processed: 83 average time/residue: 0.4255 time to fit residues: 36.7231 Evaluate side-chains 90 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN F 79 GLN G 79 GLN H 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.157635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.137413 restraints weight = 4445.652| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.50 r_work: 0.3991 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3660 Z= 0.128 Angle : 0.492 3.371 4960 Z= 0.281 Chirality : 0.050 0.133 670 Planarity : 0.002 0.007 620 Dihedral : 4.833 12.614 530 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.97 % Allowed : 21.35 % Favored : 75.68 % 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: -2.66 (0.30), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE I 94 HIS 0.005 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3660) covalent geometry : angle 0.49198 ( 4960) hydrogen bonds : bond 0.01522 ( 64) hydrogen bonds : angle 4.42136 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.122 Fit side-chains REVERT: A 60 LYS cc_start: 0.8066 (tttm) cc_final: 0.7696 (mtpt) REVERT: B 60 LYS cc_start: 0.7962 (tttm) cc_final: 0.7618 (mtpt) REVERT: B 87 SER cc_start: 0.8827 (m) cc_final: 0.8618 (t) REVERT: C 60 LYS cc_start: 0.8059 (tttm) cc_final: 0.7658 (mttm) REVERT: D 60 LYS cc_start: 0.8072 (tttm) cc_final: 0.7525 (mtpt) REVERT: D 62 GLN cc_start: 0.7760 (tt0) cc_final: 0.7492 (tm-30) REVERT: E 60 LYS cc_start: 0.8183 (tttm) cc_final: 0.7830 (mttt) REVERT: F 60 LYS cc_start: 0.7923 (tttm) cc_final: 0.7472 (mtpt) REVERT: G 60 LYS cc_start: 0.8074 (tttm) cc_final: 0.7752 (mtmt) REVERT: H 60 LYS cc_start: 0.8041 (tttm) cc_final: 0.7584 (mttt) REVERT: I 46 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: J 46 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6588 (tt0) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.4309 time to fit residues: 34.5018 Evaluate side-chains 79 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 chunk 40 optimal weight: 0.0040 overall best weight: 0.7914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN G 79 GLN H 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.159292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.138773 restraints weight = 4357.952| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.48 r_work: 0.3993 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3660 Z= 0.124 Angle : 0.484 3.388 4960 Z= 0.276 Chirality : 0.050 0.132 670 Planarity : 0.002 0.012 620 Dihedral : 4.778 14.119 530 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.24 % Allowed : 21.35 % Favored : 75.41 % 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: -2.63 (0.30), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.004 PHE B 94 HIS 0.005 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3660) covalent geometry : angle 0.48357 ( 4960) hydrogen bonds : bond 0.01427 ( 64) hydrogen bonds : angle 4.36962 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.150 Fit side-chains REVERT: A 60 LYS cc_start: 0.8025 (tttm) cc_final: 0.7569 (mtpt) REVERT: B 60 LYS cc_start: 0.7918 (tttm) cc_final: 0.7463 (mtpt) REVERT: B 87 SER cc_start: 0.8821 (m) cc_final: 0.8534 (t) REVERT: C 60 LYS cc_start: 0.7981 (tttm) cc_final: 0.7507 (mttm) REVERT: D 60 LYS cc_start: 0.8004 (tttm) cc_final: 0.7353 (mtpt) REVERT: D 62 GLN cc_start: 0.7780 (tt0) cc_final: 0.7381 (tm-30) REVERT: E 60 LYS cc_start: 0.8142 (tttm) cc_final: 0.7675 (mttt) REVERT: F 60 LYS cc_start: 0.7855 (tttm) cc_final: 0.7303 (mtpt) REVERT: G 60 LYS cc_start: 0.8042 (tttm) cc_final: 0.7612 (mtmt) REVERT: H 60 LYS cc_start: 0.7989 (tttm) cc_final: 0.7442 (mttt) REVERT: I 46 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6273 (mt-10) REVERT: J 46 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6417 (tt0) outliers start: 12 outliers final: 7 residues processed: 78 average time/residue: 0.4585 time to fit residues: 37.1386 Evaluate side-chains 80 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 62 GLN G 79 GLN H 62 GLN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.152464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.131567 restraints weight = 4454.629| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.51 r_work: 0.3911 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3660 Z= 0.282 Angle : 0.652 4.388 4960 Z= 0.368 Chirality : 0.053 0.139 670 Planarity : 0.002 0.010 620 Dihedral : 5.693 18.873 530 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.97 % Allowed : 21.89 % Favored : 75.14 % 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: -2.55 (0.31), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE I 94 HIS 0.008 0.005 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 3660) covalent geometry : angle 0.65165 ( 4960) hydrogen bonds : bond 0.02070 ( 64) hydrogen bonds : angle 4.74320 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.148 Fit side-chains REVERT: A 60 LYS cc_start: 0.8080 (tttm) cc_final: 0.7646 (mttt) REVERT: B 60 LYS cc_start: 0.8010 (tttm) cc_final: 0.7584 (mttm) REVERT: B 87 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8574 (t) REVERT: C 60 LYS cc_start: 0.8007 (tttm) cc_final: 0.7579 (mttm) REVERT: D 60 LYS cc_start: 0.8052 (tttm) cc_final: 0.7470 (mttt) REVERT: D 62 GLN cc_start: 0.7808 (tt0) cc_final: 0.7392 (tm-30) REVERT: E 60 LYS cc_start: 0.8227 (tttm) cc_final: 0.7809 (mtpt) REVERT: F 60 LYS cc_start: 0.7930 (tttm) cc_final: 0.7416 (mtpt) REVERT: G 60 LYS cc_start: 0.8062 (tttm) cc_final: 0.7649 (mtmt) REVERT: G 92 THR cc_start: 0.7612 (p) cc_final: 0.7231 (t) REVERT: H 60 LYS cc_start: 0.8016 (tttm) cc_final: 0.7485 (mttt) REVERT: I 46 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5901 (mt-10) REVERT: J 46 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6573 (tt0) outliers start: 11 outliers final: 7 residues processed: 77 average time/residue: 0.4179 time to fit residues: 33.4776 Evaluate side-chains 81 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 62 GLN H 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.160744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.140469 restraints weight = 4447.869| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.52 r_work: 0.4032 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3660 Z= 0.097 Angle : 0.455 3.275 4960 Z= 0.261 Chirality : 0.050 0.130 670 Planarity : 0.002 0.011 620 Dihedral : 4.505 12.942 530 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.35 % Allowed : 23.24 % Favored : 75.41 % 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: -2.65 (0.30), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.004 PHE B 94 HIS 0.004 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 3660) covalent geometry : angle 0.45470 ( 4960) hydrogen bonds : bond 0.01341 ( 64) hydrogen bonds : angle 4.27750 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.158 Fit side-chains REVERT: A 60 LYS cc_start: 0.8057 (tttm) cc_final: 0.7722 (mtpt) REVERT: B 60 LYS cc_start: 0.8002 (tttm) cc_final: 0.7673 (mtpt) REVERT: C 60 LYS cc_start: 0.8030 (tttm) cc_final: 0.7687 (mttm) REVERT: D 60 LYS cc_start: 0.8081 (tttm) cc_final: 0.7555 (mtpt) REVERT: D 62 GLN cc_start: 0.7759 (tt0) cc_final: 0.7517 (tm-30) REVERT: E 60 LYS cc_start: 0.8199 (tttm) cc_final: 0.7875 (mtpt) REVERT: F 60 LYS cc_start: 0.7907 (tttm) cc_final: 0.7507 (mtpt) REVERT: G 60 LYS cc_start: 0.8080 (tttm) cc_final: 0.7790 (mtpt) REVERT: H 60 LYS cc_start: 0.8057 (tttm) cc_final: 0.7627 (mttt) REVERT: I 46 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: J 46 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5807 (tt0) outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 0.2901 time to fit residues: 22.6251 Evaluate side-chains 73 residues out of total 370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN E 62 GLN H 62 GLN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.158475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.137721 restraints weight = 4362.882| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.50 r_work: 0.3981 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3660 Z= 0.139 Angle : 0.501 3.401 4960 Z= 0.287 Chirality : 0.050 0.133 670 Planarity : 0.002 0.008 620 Dihedral : 4.832 12.935 530 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.35 % Allowed : 24.32 % Favored : 74.32 % 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: -2.63 (0.30), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE C 94 HIS 0.006 0.003 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3660) covalent geometry : angle 0.50082 ( 4960) hydrogen bonds : bond 0.01457 ( 64) hydrogen bonds : angle 4.26908 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1372.06 seconds wall clock time: 24 minutes 28.54 seconds (1468.54 seconds total)