Starting phenix.real_space_refine on Tue Mar 3 12:05:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pes_20331/03_2026/6pes_20331.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pes_20331/03_2026/6pes_20331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pes_20331/03_2026/6pes_20331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pes_20331/03_2026/6pes_20331.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pes_20331/03_2026/6pes_20331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pes_20331/03_2026/6pes_20331.map" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 1.000 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 2515 2.51 5 N 700 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4040 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "W" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 367 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Restraints were copied for chains: B, C, D, E, V, X, Y, Z Time building chain proxies: 0.58, per 1000 atoms: 0.14 Number of scatterers: 4040 At special positions: 0 Unit cell: (73.485, 117.15, 43.665, 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 825 8.00 N 700 7.00 C 2515 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: 0.34 Conformation dependent library (CDL) restraints added in 116.0 milliseconds 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 64.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.324A pdb=" N VAL B 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL D 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 57 removed outlier: 6.442A pdb=" N THR B 44 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY D 47 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N GLY D 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ALA D 53 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL D 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 44 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLY B 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLU A 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL B 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA B 53 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN C 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN E 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.538A pdb=" N GLU B 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR D 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL D 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.543A pdb=" N VAL B 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 74 through 83 removed outlier: 6.361A pdb=" N VAL B 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL D 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA B 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLN D 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR D 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS B 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 10.169A pdb=" N GLU D 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N VAL B 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL B 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLN B 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR B 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LYS A 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N GLU B 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL A 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL C 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU A 83 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR C 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL E 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU C 83 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 88 through 96 removed outlier: 6.641A pdb=" N ILE B 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA D 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA B 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N GLY D 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N THR B 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N VAL D 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE B 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N VAL B 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR C 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY A 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA C 91 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR E 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY C 93 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'W' and resid 45 through 56 removed outlier: 6.885A pdb=" N VAL V 48 " --> pdb=" O GLY W 47 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL W 49 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN V 50 " --> pdb=" O VAL W 49 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL X 48 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL V 49 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN X 50 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL Y 48 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL X 49 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLN Y 50 " --> pdb=" O VAL X 49 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL Z 48 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL Y 49 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN Z 50 " --> pdb=" O VAL Y 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 61 through 66 Processing sheet with id=AA9, first strand: chain 'W' and resid 69 through 71 Processing sheet with id=AB1, first strand: chain 'W' and resid 74 through 83 removed outlier: 8.950A pdb=" N VAL W 74 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N VAL V 77 " --> pdb=" O VAL W 74 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ALA W 76 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N GLN V 79 " --> pdb=" O ALA W 76 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA W 78 " --> pdb=" O GLN V 79 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N THR V 81 " --> pdb=" O ALA W 78 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS W 80 " --> pdb=" O THR V 81 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLU V 83 " --> pdb=" O LYS W 80 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL W 82 " --> pdb=" O GLU V 83 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N VAL V 74 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N VAL X 77 " --> pdb=" O VAL V 74 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ALA V 76 " --> pdb=" O VAL X 77 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLN X 79 " --> pdb=" O ALA V 76 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N ALA V 78 " --> pdb=" O GLN X 79 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N THR X 81 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS V 80 " --> pdb=" O THR X 81 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLU X 83 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL V 82 " --> pdb=" O GLU X 83 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL X 74 " --> pdb=" O THR Y 75 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N VAL Y 77 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ALA X 76 " --> pdb=" O VAL Y 77 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N GLN Y 79 " --> pdb=" O ALA X 76 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ALA X 78 " --> pdb=" O GLN Y 79 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N THR Y 81 " --> pdb=" O ALA X 78 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS X 80 " --> pdb=" O THR Y 81 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU Y 83 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL X 82 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL Y 74 " --> pdb=" O THR Z 75 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N VAL Z 77 " --> pdb=" O VAL Y 74 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N ALA Y 76 " --> pdb=" O VAL Z 77 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N GLN Z 79 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA Y 78 " --> pdb=" O GLN Z 79 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N THR Z 81 " --> pdb=" O ALA Y 78 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS Y 80 " --> pdb=" O THR Z 81 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU Z 83 " --> pdb=" O LYS Y 80 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL Y 82 " --> pdb=" O GLU Z 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'W' and resid 88 through 96 removed outlier: 8.432A pdb=" N ALA W 89 " --> pdb=" O ALA V 90 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR V 92 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N ALA W 91 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N PHE V 94 " --> pdb=" O ALA W 91 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY W 93 " --> pdb=" O PHE V 94 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS V 96 " --> pdb=" O GLY W 93 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL W 95 " --> pdb=" O LYS V 96 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ALA V 89 " --> pdb=" O ALA X 90 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR X 92 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N ALA V 91 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N PHE X 94 " --> pdb=" O ALA V 91 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY V 93 " --> pdb=" O PHE X 94 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LYS X 96 " --> pdb=" O GLY V 93 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL V 95 " --> pdb=" O LYS X 96 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ALA X 89 " --> pdb=" O ALA Y 90 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR Y 92 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N ALA X 91 " --> pdb=" O THR Y 92 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE Y 94 " --> pdb=" O ALA X 91 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY X 93 " --> pdb=" O PHE Y 94 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LYS Y 96 " --> pdb=" O GLY X 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL X 95 " --> pdb=" O LYS Y 96 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ALA Y 89 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR Z 92 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ALA Y 91 " --> pdb=" O THR Z 92 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N PHE Z 94 " --> pdb=" O ALA Y 91 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY Y 93 " --> pdb=" O PHE Z 94 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS Z 96 " --> pdb=" O GLY Y 93 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL Y 95 " --> pdb=" O LYS Z 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 124 hydrogen bonds defined for protein. 372 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: 0.48 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 725 1.29 - 1.35: 625 1.35 - 1.42: 110 1.42 - 1.48: 689 1.48 - 1.54: 1896 Bond restraints: 4045 Sorted by residual: bond pdb=" CB VAL Z 66 " pdb=" CG2 VAL Z 66 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CB VAL Y 66 " pdb=" CG2 VAL Y 66 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CB VAL W 66 " pdb=" CG2 VAL W 66 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.95e+00 bond pdb=" CB VAL V 66 " pdb=" CG2 VAL V 66 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.87e+00 bond pdb=" CB VAL X 66 " pdb=" CG2 VAL X 66 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.82e+00 ... (remaining 4040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.68: 4266 0.68 - 1.36: 842 1.36 - 2.04: 209 2.04 - 2.72: 112 2.72 - 3.39: 36 Bond angle restraints: 5465 Sorted by residual: angle pdb=" C THR Z 59 " pdb=" N LYS Z 60 " pdb=" CA LYS Z 60 " ideal model delta sigma weight residual 122.93 119.54 3.39 1.51e+00 4.39e-01 5.05e+00 angle pdb=" C THR W 59 " pdb=" N LYS W 60 " pdb=" CA LYS W 60 " ideal model delta sigma weight residual 122.93 119.54 3.39 1.51e+00 4.39e-01 5.03e+00 angle pdb=" C THR V 59 " pdb=" N LYS V 60 " pdb=" CA LYS V 60 " ideal model delta sigma weight residual 122.93 119.55 3.38 1.51e+00 4.39e-01 5.00e+00 angle pdb=" C THR X 59 " pdb=" N LYS X 60 " pdb=" CA LYS X 60 " ideal model delta sigma weight residual 122.93 119.57 3.36 1.51e+00 4.39e-01 4.96e+00 angle pdb=" C THR Y 59 " pdb=" N LYS Y 60 " pdb=" CA LYS Y 60 " ideal model delta sigma weight residual 122.93 119.57 3.36 1.51e+00 4.39e-01 4.95e+00 ... (remaining 5460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.69: 2095 12.69 - 25.39: 220 25.39 - 38.08: 40 38.08 - 50.77: 15 50.77 - 63.46: 15 Dihedral angle restraints: 2385 sinusoidal: 800 harmonic: 1585 Sorted by residual: dihedral pdb=" CA VAL E 48 " pdb=" C VAL E 48 " pdb=" N VAL E 49 " pdb=" CA VAL E 49 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA VAL D 48 " pdb=" C VAL D 48 " pdb=" N VAL D 49 " pdb=" CA VAL D 49 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA VAL C 48 " pdb=" C VAL C 48 " pdb=" N VAL C 49 " pdb=" CA VAL C 49 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 2382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 517 0.052 - 0.103: 132 0.103 - 0.155: 71 0.155 - 0.206: 0 0.206 - 0.258: 5 Chirality restraints: 725 Sorted by residual: chirality pdb=" CB VAL Y 66 " pdb=" CA VAL Y 66 " pdb=" CG1 VAL Y 66 " pdb=" CG2 VAL Y 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL V 66 " pdb=" CA VAL V 66 " pdb=" CG1 VAL V 66 " pdb=" CG2 VAL V 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL X 66 " pdb=" CA VAL X 66 " pdb=" CG1 VAL X 66 " pdb=" CG2 VAL X 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 722 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS Y 60 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C LYS Y 60 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS Y 60 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU Y 61 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS W 60 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS W 60 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS W 60 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU W 61 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS X 60 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LYS X 60 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS X 60 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU X 61 " 0.023 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 1854 2.93 - 3.42: 3431 3.42 - 3.91: 6356 3.91 - 4.41: 6980 4.41 - 4.90: 13933 Nonbonded interactions: 32554 Sorted by model distance: nonbonded pdb=" NZ LYS X 58 " pdb=" OE2 GLU X 61 " model vdw 2.432 3.120 nonbonded pdb=" NZ LYS W 58 " pdb=" OE2 GLU W 61 " model vdw 2.432 3.120 nonbonded pdb=" NZ LYS V 58 " pdb=" OE2 GLU V 61 " model vdw 2.432 3.120 nonbonded pdb=" NZ LYS Y 58 " pdb=" OE2 GLU Y 61 " model vdw 2.432 3.120 nonbonded pdb=" NZ LYS Z 58 " pdb=" OE2 GLU Z 61 " model vdw 2.433 3.120 ... (remaining 32549 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'W' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.920 Find NCS groups from input model: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.009 0.104 4045 Z= 0.385 Angle : 0.704 3.394 5465 Z= 0.422 Chirality : 0.060 0.258 725 Planarity : 0.007 0.040 685 Dihedral : 12.873 63.461 1385 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % 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: -1.79 (0.32), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR D 39 PHE 0.016 0.004 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00889 ( 4045) covalent geometry : angle 0.70409 ( 5465) hydrogen bonds : bond 0.12408 ( 124) hydrogen bonds : angle 9.36779 ( 372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.148 Fit side-chains REVERT: A 50 GLN cc_start: 0.8054 (tp40) cc_final: 0.7288 (tp40) REVERT: A 72 THR cc_start: 0.9263 (m) cc_final: 0.9060 (m) REVERT: D 80 LYS cc_start: 0.8383 (tttm) cc_final: 0.6859 (pttt) REVERT: E 45 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7362 (mtpp) REVERT: E 50 GLN cc_start: 0.8001 (tp40) cc_final: 0.6919 (tp40) REVERT: W 45 LYS cc_start: 0.7344 (mtmt) cc_final: 0.6595 (mtpp) REVERT: W 83 GLU cc_start: 0.7399 (pm20) cc_final: 0.6912 (mp0) REVERT: V 45 LYS cc_start: 0.7120 (mtmt) cc_final: 0.6241 (mtpp) REVERT: V 83 GLU cc_start: 0.7726 (pm20) cc_final: 0.7103 (mp0) REVERT: X 45 LYS cc_start: 0.7514 (mtmt) cc_final: 0.6678 (mtpp) REVERT: X 83 GLU cc_start: 0.7381 (pm20) cc_final: 0.7017 (pm20) REVERT: Y 81 THR cc_start: 0.8136 (t) cc_final: 0.7590 (t) REVERT: Y 83 GLU cc_start: 0.7486 (pm20) cc_final: 0.6913 (mp0) REVERT: Z 45 LYS cc_start: 0.7525 (mtmt) cc_final: 0.6983 (mtpp) REVERT: Z 83 GLU cc_start: 0.7690 (pm20) cc_final: 0.7119 (mp0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0807 time to fit residues: 7.8532 Evaluate side-chains 71 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN C 99 GLN D 99 GLN W 50 GLN V 50 GLN X 50 GLN Y 50 GLN Z 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.193499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.171919 restraints weight = 4669.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.175448 restraints weight = 1870.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.177870 restraints weight = 1045.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.179235 restraints weight = 720.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.180155 restraints weight = 579.533| |-----------------------------------------------------------------------------| r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4045 Z= 0.142 Angle : 0.469 3.268 5465 Z= 0.274 Chirality : 0.055 0.130 725 Planarity : 0.002 0.016 685 Dihedral : 4.737 15.053 585 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.37 % Allowed : 13.17 % Favored : 81.46 % 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: -1.80 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 39 PHE 0.010 0.002 PHE A 94 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4045) covalent geometry : angle 0.46867 ( 5465) hydrogen bonds : bond 0.02984 ( 124) hydrogen bonds : angle 6.56975 ( 372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.139 Fit side-chains REVERT: A 72 THR cc_start: 0.9168 (m) cc_final: 0.8919 (m) REVERT: A 99 GLN cc_start: 0.5148 (OUTLIER) cc_final: 0.4886 (tt0) REVERT: B 50 GLN cc_start: 0.7844 (tp40) cc_final: 0.7561 (tp40) REVERT: B 71 VAL cc_start: 0.9026 (t) cc_final: 0.8747 (m) REVERT: D 80 LYS cc_start: 0.8564 (tttm) cc_final: 0.7099 (pttt) REVERT: E 50 GLN cc_start: 0.8217 (tp40) cc_final: 0.6659 (pm20) REVERT: E 66 VAL cc_start: 0.9051 (t) cc_final: 0.8825 (m) REVERT: W 45 LYS cc_start: 0.7472 (mtmt) cc_final: 0.6829 (mtpp) REVERT: V 45 LYS cc_start: 0.7618 (mtmt) cc_final: 0.6872 (mtpp) REVERT: V 83 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: X 45 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7244 (mtpp) REVERT: X 83 GLU cc_start: 0.7704 (pm20) cc_final: 0.7176 (mp0) REVERT: X 94 PHE cc_start: 0.7693 (t80) cc_final: 0.7434 (t80) REVERT: Y 45 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7085 (mtpp) REVERT: Y 83 GLU cc_start: 0.7964 (pm20) cc_final: 0.7494 (mp0) REVERT: Z 45 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7383 (mtpp) REVERT: Z 83 GLU cc_start: 0.7980 (pm20) cc_final: 0.7694 (mp0) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.0641 time to fit residues: 7.5978 Evaluate side-chains 94 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 30.0000 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN D 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.193158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.171433 restraints weight = 4690.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.175001 restraints weight = 1900.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.177393 restraints weight = 1059.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.178798 restraints weight = 731.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.179856 restraints weight = 589.665| |-----------------------------------------------------------------------------| r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4045 Z= 0.141 Angle : 0.449 3.160 5465 Z= 0.260 Chirality : 0.054 0.131 725 Planarity : 0.002 0.013 685 Dihedral : 4.579 14.489 585 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.83 % Allowed : 15.61 % Favored : 77.56 % 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: -1.86 (0.32), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.018 0.003 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4045) covalent geometry : angle 0.44860 ( 5465) hydrogen bonds : bond 0.02676 ( 124) hydrogen bonds : angle 5.89490 ( 372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.143 Fit side-chains REVERT: B 48 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8602 (p) REVERT: B 71 VAL cc_start: 0.9031 (t) cc_final: 0.8730 (m) REVERT: B 72 THR cc_start: 0.9123 (m) cc_final: 0.8894 (m) REVERT: D 80 LYS cc_start: 0.8574 (tttm) cc_final: 0.7047 (pttt) REVERT: E 50 GLN cc_start: 0.8202 (tp40) cc_final: 0.6657 (pm20) REVERT: E 66 VAL cc_start: 0.9061 (t) cc_final: 0.8841 (m) REVERT: W 45 LYS cc_start: 0.7516 (mtmt) cc_final: 0.6925 (mtpp) REVERT: V 45 LYS cc_start: 0.7643 (mtmt) cc_final: 0.6924 (mtpp) REVERT: V 83 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: X 45 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7362 (mtpp) REVERT: Y 45 LYS cc_start: 0.7805 (mtmt) cc_final: 0.7045 (mtpp) REVERT: Y 83 GLU cc_start: 0.7949 (pm20) cc_final: 0.7643 (mp0) REVERT: Z 45 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7444 (mtpp) REVERT: Z 83 GLU cc_start: 0.7824 (pm20) cc_final: 0.7567 (mp0) outliers start: 28 outliers final: 19 residues processed: 88 average time/residue: 0.0627 time to fit residues: 7.0787 Evaluate side-chains 96 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN E 99 GLN ** W 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 = 0.4741 r_free = 0.4741 target = 0.191793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.170420 restraints weight = 4612.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.173932 restraints weight = 1858.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.176275 restraints weight = 1039.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.177576 restraints weight = 723.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.178595 restraints weight = 587.388| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4045 Z= 0.164 Angle : 0.463 5.305 5465 Z= 0.266 Chirality : 0.054 0.128 725 Planarity : 0.002 0.011 685 Dihedral : 4.612 17.874 585 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 6.10 % Allowed : 15.61 % Favored : 78.29 % 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: -1.99 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.019 0.003 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4045) covalent geometry : angle 0.46346 ( 5465) hydrogen bonds : bond 0.02617 ( 124) hydrogen bonds : angle 5.67389 ( 372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.098 Fit side-chains REVERT: D 80 LYS cc_start: 0.8592 (tttm) cc_final: 0.7153 (pttt) REVERT: E 50 GLN cc_start: 0.8190 (tp40) cc_final: 0.6742 (pm20) REVERT: W 45 LYS cc_start: 0.7675 (mtmt) cc_final: 0.7075 (mtpp) REVERT: V 45 LYS cc_start: 0.7737 (mtmt) cc_final: 0.7016 (mtpp) REVERT: X 45 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7441 (mtpp) REVERT: Y 45 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7249 (mtpp) REVERT: Y 83 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: Z 45 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7562 (mtpp) outliers start: 25 outliers final: 18 residues processed: 86 average time/residue: 0.0583 time to fit residues: 6.4624 Evaluate side-chains 94 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 83 GLU Chi-restraints excluded: chain Z residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 37 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 20.0000 overall best weight: 6.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.189568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.168252 restraints weight = 4617.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.171720 restraints weight = 1854.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.173843 restraints weight = 1039.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.175357 restraints weight = 738.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.176075 restraints weight = 586.258| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4045 Z= 0.186 Angle : 0.475 4.244 5465 Z= 0.273 Chirality : 0.054 0.132 725 Planarity : 0.002 0.011 685 Dihedral : 4.671 16.641 585 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 6.10 % Allowed : 15.85 % Favored : 78.05 % 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: -2.14 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 39 PHE 0.019 0.003 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4045) covalent geometry : angle 0.47506 ( 5465) hydrogen bonds : bond 0.02654 ( 124) hydrogen bonds : angle 5.53871 ( 372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.114 Fit side-chains REVERT: A 72 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8796 (m) REVERT: D 80 LYS cc_start: 0.8590 (tttm) cc_final: 0.7187 (pttt) REVERT: E 50 GLN cc_start: 0.8198 (tp40) cc_final: 0.6991 (pt0) REVERT: W 45 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7063 (mtpp) REVERT: V 45 LYS cc_start: 0.7739 (mtmt) cc_final: 0.7030 (mtpp) REVERT: X 45 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7430 (mtpp) REVERT: Y 45 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7240 (mtpp) REVERT: Y 83 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: Z 45 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7750 (mtpp) REVERT: Z 83 GLU cc_start: 0.7819 (mp0) cc_final: 0.7560 (mp0) outliers start: 25 outliers final: 20 residues processed: 89 average time/residue: 0.0644 time to fit residues: 7.2773 Evaluate side-chains 97 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 83 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 38 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 overall best weight: 11.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.182924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.160927 restraints weight = 4849.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.164383 restraints weight = 1931.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.166666 restraints weight = 1087.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.168155 restraints weight = 760.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.168728 restraints weight = 607.291| |-----------------------------------------------------------------------------| r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 4045 Z= 0.312 Angle : 0.574 4.551 5465 Z= 0.333 Chirality : 0.057 0.136 725 Planarity : 0.003 0.009 685 Dihedral : 5.154 17.694 585 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 7.07 % Allowed : 14.88 % Favored : 78.05 % 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: -2.50 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.021 0.004 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00701 ( 4045) covalent geometry : angle 0.57416 ( 5465) hydrogen bonds : bond 0.03286 ( 124) hydrogen bonds : angle 5.72882 ( 372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.134 Fit side-chains REVERT: B 45 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8078 (mtpt) REVERT: E 50 GLN cc_start: 0.8253 (tp40) cc_final: 0.7046 (pt0) REVERT: W 45 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7190 (mtpp) REVERT: V 45 LYS cc_start: 0.7734 (mtmt) cc_final: 0.6980 (mtpp) REVERT: V 83 GLU cc_start: 0.7965 (mp0) cc_final: 0.7629 (mp0) REVERT: X 45 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7363 (mtpp) REVERT: X 50 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: Y 45 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7164 (mtpp) REVERT: Y 50 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7665 (tp40) REVERT: Z 45 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7657 (mtpp) REVERT: Z 83 GLU cc_start: 0.7929 (mp0) cc_final: 0.7686 (mp0) outliers start: 29 outliers final: 21 residues processed: 87 average time/residue: 0.0652 time to fit residues: 7.1994 Evaluate side-chains 94 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain X residue 50 GLN Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.187143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.165446 restraints weight = 4781.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.168971 restraints weight = 1893.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.171323 restraints weight = 1055.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.172763 restraints weight = 732.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.173679 restraints weight = 583.017| |-----------------------------------------------------------------------------| r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4045 Z= 0.153 Angle : 0.461 3.827 5465 Z= 0.265 Chirality : 0.054 0.141 725 Planarity : 0.002 0.011 685 Dihedral : 4.564 16.447 585 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.61 % Allowed : 16.34 % Favored : 78.05 % 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: -2.42 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 39 PHE 0.018 0.003 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4045) covalent geometry : angle 0.46071 ( 5465) hydrogen bonds : bond 0.02510 ( 124) hydrogen bonds : angle 5.33405 ( 372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.098 Fit side-chains REVERT: A 72 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8820 (m) REVERT: E 50 GLN cc_start: 0.8229 (tp40) cc_final: 0.7011 (pt0) REVERT: W 45 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7112 (mtpp) REVERT: V 45 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7033 (mtpp) REVERT: X 45 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7368 (mtpp) REVERT: Y 45 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7241 (mtpp) REVERT: Y 50 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7796 (tp40) REVERT: Z 45 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7783 (mtpp) REVERT: Z 83 GLU cc_start: 0.8035 (mp0) cc_final: 0.7782 (mp0) outliers start: 23 outliers final: 16 residues processed: 86 average time/residue: 0.0624 time to fit residues: 6.8101 Evaluate side-chains 93 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 40.0000 chunk 27 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 overall best weight: 8.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.184660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.162894 restraints weight = 4729.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.166324 restraints weight = 1889.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.168607 restraints weight = 1064.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.170074 restraints weight = 746.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.170675 restraints weight = 596.838| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 4045 Z= 0.221 Angle : 0.529 9.519 5465 Z= 0.298 Chirality : 0.055 0.136 725 Planarity : 0.002 0.014 685 Dihedral : 4.798 18.372 585 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.12 % Allowed : 17.07 % Favored : 77.80 % 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: -2.51 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.022 0.003 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 4045) covalent geometry : angle 0.52921 ( 5465) hydrogen bonds : bond 0.02825 ( 124) hydrogen bonds : angle 5.43404 ( 372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.134 Fit side-chains REVERT: A 72 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8847 (m) REVERT: E 50 GLN cc_start: 0.8245 (tp40) cc_final: 0.7031 (pt0) REVERT: W 45 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7094 (mtpp) REVERT: V 45 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7030 (mtpp) REVERT: X 45 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7346 (mtpp) REVERT: X 50 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7728 (tp40) REVERT: Y 45 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7278 (mtpp) REVERT: Y 50 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7586 (tp40) REVERT: Z 45 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7806 (mtpt) REVERT: Z 50 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (tp40) REVERT: Z 83 GLU cc_start: 0.8049 (mp0) cc_final: 0.7775 (mp0) outliers start: 21 outliers final: 15 residues processed: 83 average time/residue: 0.0619 time to fit residues: 6.5551 Evaluate side-chains 90 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain X residue 50 GLN Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 50.0000 chunk 45 optimal weight: 40.0000 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 40.0000 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.185906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.163884 restraints weight = 4781.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.167305 restraints weight = 1903.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.169382 restraints weight = 1074.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.170859 restraints weight = 771.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.171897 restraints weight = 620.553| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4045 Z= 0.202 Angle : 0.519 8.873 5465 Z= 0.292 Chirality : 0.055 0.137 725 Planarity : 0.002 0.017 685 Dihedral : 4.687 17.611 585 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.61 % Allowed : 16.83 % Favored : 77.56 % 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: -2.52 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR E 39 PHE 0.022 0.003 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 4045) covalent geometry : angle 0.51877 ( 5465) hydrogen bonds : bond 0.02719 ( 124) hydrogen bonds : angle 5.36964 ( 372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.136 Fit side-chains REVERT: A 72 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8840 (m) REVERT: E 50 GLN cc_start: 0.8234 (tp40) cc_final: 0.7019 (pt0) REVERT: W 45 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7142 (mtpp) REVERT: V 45 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7037 (mtpp) REVERT: X 45 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7322 (mtpp) REVERT: X 50 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7622 (tp40) REVERT: Y 45 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7283 (mtpp) REVERT: Y 50 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7564 (tp40) REVERT: Z 45 LYS cc_start: 0.8357 (mtmt) cc_final: 0.7901 (mtpt) REVERT: Z 50 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8017 (tp40) REVERT: Z 83 GLU cc_start: 0.8046 (mp0) cc_final: 0.7780 (mp0) outliers start: 23 outliers final: 18 residues processed: 79 average time/residue: 0.0571 time to fit residues: 5.8354 Evaluate side-chains 90 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain X residue 50 GLN Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 51 optimal weight: 0.0000 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 overall best weight: 4.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** Z 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 = 0.4740 r_free = 0.4740 target = 0.189028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.167111 restraints weight = 4697.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.170559 restraints weight = 1876.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.172831 restraints weight = 1048.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.174364 restraints weight = 737.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.175249 restraints weight = 586.003| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4045 Z= 0.123 Angle : 0.470 9.009 5465 Z= 0.262 Chirality : 0.054 0.135 725 Planarity : 0.002 0.015 685 Dihedral : 4.336 17.407 585 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.15 % Allowed : 17.80 % Favored : 78.05 % 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 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR E 39 PHE 0.022 0.003 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4045) covalent geometry : angle 0.47017 ( 5465) hydrogen bonds : bond 0.02243 ( 124) hydrogen bonds : angle 5.11472 ( 372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.092 Fit side-chains REVERT: A 72 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8823 (m) REVERT: B 48 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8755 (p) REVERT: E 50 GLN cc_start: 0.8208 (tp40) cc_final: 0.6978 (pt0) REVERT: W 45 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7068 (mtpp) REVERT: V 45 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7007 (mtpp) REVERT: X 45 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7344 (mtpp) REVERT: Y 45 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7226 (mtpp) REVERT: Z 45 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7748 (mtpp) REVERT: Z 83 GLU cc_start: 0.8074 (mp0) cc_final: 0.7839 (mp0) outliers start: 17 outliers final: 12 residues processed: 78 average time/residue: 0.0563 time to fit residues: 5.7326 Evaluate side-chains 82 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 54 optimal weight: 50.0000 chunk 36 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 43 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 overall best weight: 12.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.182293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.160129 restraints weight = 4825.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.163534 restraints weight = 1944.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.165848 restraints weight = 1108.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.167259 restraints weight = 781.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.168255 restraints weight = 631.165| |-----------------------------------------------------------------------------| r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 4045 Z= 0.325 Angle : 0.613 8.407 5465 Z= 0.348 Chirality : 0.057 0.142 725 Planarity : 0.003 0.016 685 Dihedral : 5.107 19.921 585 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.39 % Allowed : 17.32 % Favored : 78.29 % 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: -2.75 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 39 PHE 0.024 0.004 PHE W 94 Details of bonding type rmsd covalent geometry : bond 0.00735 ( 4045) covalent geometry : angle 0.61279 ( 5465) hydrogen bonds : bond 0.03345 ( 124) hydrogen bonds : angle 5.56112 ( 372) =============================================================================== Job complete usr+sys time: 694.43 seconds wall clock time: 12 minutes 45.99 seconds (765.99 seconds total)