Starting phenix.real_space_refine on Tue Feb 11 03:02:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pes_20331/02_2025/6pes_20331.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pes_20331/02_2025/6pes_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pes_20331/02_2025/6pes_20331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pes_20331/02_2025/6pes_20331.map" model { file = "/net/cci-nas-00/data/ceres_data/6pes_20331/02_2025/6pes_20331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pes_20331/02_2025/6pes_20331.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D, V, Y, X, Z Time building chain proxies: 1.75, per 1000 atoms: 0.43 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: 0.98 Conformation dependent library (CDL) restraints added in 566.4 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: 0.67 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: 1.04 Time building geometry restraints manager: 1.14 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.080 Find NCS groups from input model: 0.100 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- 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= 0.595 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 : 11.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 PHE 0.016 0.004 PHE W 94 TYR 0.002 0.001 TYR D 39 *********************** 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 : 0.460 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: 0.6918 (tp40) REVERT: W 45 LYS cc_start: 0.7344 (mtmt) cc_final: 0.6595 (mtpp) REVERT: W 83 GLU cc_start: 0.7398 (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: 0.8135 (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: 0.7689 (pm20) cc_final: 0.7119 (mp0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1929 time to fit residues: 18.6205 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 : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.188955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.167003 restraints weight = 4698.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.170534 restraints weight = 1914.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.172850 restraints weight = 1077.876| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1406 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= 0.369 Angle : 0.531 3.469 5465 Z= 0.311 Chirality : 0.056 0.132 725 Planarity : 0.003 0.016 685 Dihedral : 5.132 16.706 585 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 5.61 % Allowed : 13.66 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE Z 94 TYR 0.004 0.001 TYR C 39 *********************** 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 104 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.444 Fit side-chains REVERT: A 72 THR cc_start: 0.9160 (m) cc_final: 0.8924 (m) REVERT: C 45 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7905 (mtpt) REVERT: C 99 GLN cc_start: 0.5590 (tt0) cc_final: 0.5252 (tt0) REVERT: D 80 LYS cc_start: 0.8623 (tttm) cc_final: 0.7187 (pttt) REVERT: E 50 GLN cc_start: 0.8240 (tp40) cc_final: 0.6949 (pt0) REVERT: W 45 LYS cc_start: 0.7523 (mtmt) cc_final: 0.6869 (mtpp) REVERT: W 83 GLU cc_start: 0.7797 (pm20) cc_final: 0.7388 (mp0) REVERT: V 45 LYS cc_start: 0.7666 (mtmt) cc_final: 0.6926 (mtpp) REVERT: V 83 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: V 94 PHE cc_start: 0.7868 (t80) cc_final: 0.7638 (t80) REVERT: X 45 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7288 (mtpp) REVERT: X 83 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: Y 45 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7087 (mtpp) REVERT: Y 83 GLU cc_start: 0.7925 (pm20) cc_final: 0.7431 (mp0) REVERT: Z 45 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7432 (mtpp) REVERT: Z 83 GLU cc_start: 0.7946 (pm20) cc_final: 0.7706 (mp0) outliers start: 23 outliers final: 16 residues processed: 88 average time/residue: 0.1800 time to fit residues: 19.8841 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 : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 87 SER 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 X residue 83 GLU Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Z 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 11 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN D 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.190846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.169144 restraints weight = 4616.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.172695 restraints weight = 1860.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.174972 restraints weight = 1039.170| |-----------------------------------------------------------------------------| r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 4045 Z= 0.245 Angle : 0.475 8.083 5465 Z= 0.271 Chirality : 0.054 0.126 725 Planarity : 0.002 0.014 685 Dihedral : 4.714 15.043 585 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 7.32 % Allowed : 14.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.003 PHE Y 94 TYR 0.005 0.001 TYR C 39 *********************** 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 108 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.573 Fit side-chains REVERT: A 72 THR cc_start: 0.9151 (m) cc_final: 0.8829 (m) REVERT: D 80 LYS cc_start: 0.8589 (tttm) cc_final: 0.7209 (pttt) REVERT: E 50 GLN cc_start: 0.8222 (tp40) cc_final: 0.6930 (pt0) REVERT: E 66 VAL cc_start: 0.9096 (t) cc_final: 0.8819 (m) REVERT: E 99 GLN cc_start: 0.5289 (tt0) cc_final: 0.5038 (tt0) REVERT: W 45 LYS cc_start: 0.7718 (mtmt) cc_final: 0.7088 (mtpp) REVERT: W 81 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8051 (m) REVERT: V 45 LYS cc_start: 0.7688 (mtmt) cc_final: 0.6967 (mtpp) REVERT: V 83 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: X 45 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7384 (mtpp) REVERT: X 83 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: Y 45 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7110 (mtpp) REVERT: Y 83 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: Z 45 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7491 (mtpp) REVERT: Z 83 GLU cc_start: 0.7938 (pm20) cc_final: 0.7629 (mp0) outliers start: 30 outliers final: 21 residues processed: 88 average time/residue: 0.1552 time to fit residues: 17.4788 Evaluate side-chains 100 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 W residue 81 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 X residue 83 GLU 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 Chi-restraints excluded: chain Z residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 54 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 overall best weight: 17.9998 ------------------------------------------------------------------------------- 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 = 0.4608 r_free = 0.4608 target = 0.179638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.157204 restraints weight = 4840.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.160522 restraints weight = 1957.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.162828 restraints weight = 1123.104| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.047 4045 Z= 0.725 Angle : 0.723 5.111 5465 Z= 0.422 Chirality : 0.061 0.142 725 Planarity : 0.003 0.013 685 Dihedral : 5.811 19.559 585 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 8.78 % Allowed : 13.90 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.29), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.005 PHE W 94 TYR 0.005 0.002 TYR E 39 *********************** 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 110 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.469 Fit side-chains REVERT: A 72 THR cc_start: 0.9263 (m) cc_final: 0.8949 (m) REVERT: E 50 GLN cc_start: 0.8397 (tp40) cc_final: 0.7057 (pt0) REVERT: W 45 LYS cc_start: 0.7653 (mtmt) cc_final: 0.7009 (mtpp) REVERT: W 50 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6565 (tm130) REVERT: V 45 LYS cc_start: 0.7735 (mtmt) cc_final: 0.6975 (mtpp) REVERT: V 83 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: X 45 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7247 (mtpp) REVERT: X 50 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7892 (tp40) REVERT: Y 45 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7206 (mtpp) REVERT: Y 50 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7767 (tp40) REVERT: Z 45 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7756 (mtpt) REVERT: Z 83 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7887 (mp0) outliers start: 36 outliers final: 23 residues processed: 90 average time/residue: 0.1647 time to fit residues: 18.5251 Evaluate side-chains 98 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 96 LYS 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 50 GLN 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 50 GLN Chi-restraints excluded: chain X residue 72 THR 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 Chi-restraints excluded: chain Z residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4682 r_free = 0.4682 target = 0.186266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.164031 restraints weight = 4799.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.167541 restraints weight = 1900.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.169857 restraints weight = 1068.269| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2329 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= 0.257 Angle : 0.503 8.676 5465 Z= 0.282 Chirality : 0.055 0.141 725 Planarity : 0.002 0.010 685 Dihedral : 4.809 18.073 585 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 7.07 % Allowed : 16.10 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE W 94 TYR 0.002 0.001 TYR A 39 *********************** 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 103 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.447 Fit side-chains REVERT: A 72 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8844 (m) REVERT: E 50 GLN cc_start: 0.8243 (tp40) cc_final: 0.7033 (pt0) REVERT: W 45 LYS cc_start: 0.7718 (mtmt) cc_final: 0.7022 (mtpp) REVERT: W 50 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6491 (tm130) REVERT: V 45 LYS cc_start: 0.7705 (mtmt) cc_final: 0.6922 (mtpp) REVERT: V 50 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7668 (tp40) REVERT: X 45 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7195 (mtpp) REVERT: X 83 GLU cc_start: 0.8004 (mp0) cc_final: 0.7676 (mp0) REVERT: Y 45 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7157 (mtpp) REVERT: Y 83 GLU cc_start: 0.7944 (mp0) cc_final: 0.7550 (mp0) REVERT: Z 45 LYS cc_start: 0.8320 (mtmt) cc_final: 0.7774 (mtpp) REVERT: Z 83 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7704 (mp0) outliers start: 29 outliers final: 18 residues processed: 87 average time/residue: 0.1631 time to fit residues: 17.7210 Evaluate side-chains 93 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 50 GLN Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.4677 r_free = 0.4677 target = 0.184252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.161682 restraints weight = 4751.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.165136 restraints weight = 1908.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.167478 restraints weight = 1084.413| |-----------------------------------------------------------------------------| r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 4045 Z= 0.363 Angle : 0.539 7.632 5465 Z= 0.304 Chirality : 0.055 0.135 725 Planarity : 0.002 0.010 685 Dihedral : 4.979 18.235 585 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 7.56 % Allowed : 15.61 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.004 PHE W 94 TYR 0.002 0.001 TYR B 39 *********************** 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: 31 poor density : 72 time to evaluate : 0.448 Fit side-chains REVERT: A 72 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8873 (m) REVERT: E 50 GLN cc_start: 0.8254 (tp40) cc_final: 0.6983 (pt0) REVERT: W 45 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7036 (mtpp) REVERT: W 50 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.6537 (tm130) REVERT: V 45 LYS cc_start: 0.7712 (mtmt) cc_final: 0.6943 (mtpp) REVERT: V 50 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7516 (tp40) REVERT: V 83 GLU cc_start: 0.8130 (mp0) cc_final: 0.7872 (mp0) REVERT: X 45 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7156 (mtpp) REVERT: X 50 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: X 83 GLU cc_start: 0.8043 (mp0) cc_final: 0.7694 (mp0) REVERT: Y 45 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7156 (mtpp) REVERT: Y 50 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7592 (tp40) REVERT: Y 83 GLU cc_start: 0.7830 (mp0) cc_final: 0.7626 (mp0) REVERT: Z 45 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7794 (mtpt) REVERT: Z 83 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7748 (mp0) outliers start: 31 outliers final: 21 residues processed: 87 average time/residue: 0.1519 time to fit residues: 16.5433 Evaluate side-chains 98 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 99 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 50 GLN Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 92 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 Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 50.0000 chunk 10 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.4683 r_free = 0.4683 target = 0.183278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.160975 restraints weight = 4778.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.164420 restraints weight = 1917.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.166726 restraints weight = 1091.856| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 4045 Z= 0.410 Angle : 0.557 6.862 5465 Z= 0.317 Chirality : 0.056 0.138 725 Planarity : 0.002 0.010 685 Dihedral : 5.073 18.276 585 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 7.32 % Allowed : 15.85 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.004 PHE W 94 TYR 0.003 0.001 TYR C 39 *********************** 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 101 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.419 Fit side-chains REVERT: E 50 GLN cc_start: 0.8242 (tp40) cc_final: 0.6997 (pt0) REVERT: W 45 LYS cc_start: 0.7814 (mtmt) cc_final: 0.7019 (mtpp) REVERT: W 50 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6514 (tm130) REVERT: V 45 LYS cc_start: 0.7744 (mtmt) cc_final: 0.6990 (mtpp) REVERT: V 50 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7584 (tp40) REVERT: X 45 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7217 (mtpp) REVERT: X 50 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7766 (tp40) REVERT: X 83 GLU cc_start: 0.8057 (mp0) cc_final: 0.7652 (mp0) REVERT: Y 45 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7200 (mtpp) REVERT: Y 50 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7652 (tp40) REVERT: Y 83 GLU cc_start: 0.7834 (mp0) cc_final: 0.7629 (mp0) REVERT: Z 45 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7790 (mtpt) REVERT: Z 83 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7761 (mp0) outliers start: 30 outliers final: 24 residues processed: 85 average time/residue: 0.1496 time to fit residues: 16.1777 Evaluate side-chains 98 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 46 GLU 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 99 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 50 GLN Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 92 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 Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.4707 r_free = 0.4707 target = 0.185554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.163189 restraints weight = 4682.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.166689 restraints weight = 1894.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.169015 restraints weight = 1078.755| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2570 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= 0.287 Angle : 0.510 6.644 5465 Z= 0.288 Chirality : 0.055 0.139 725 Planarity : 0.002 0.010 685 Dihedral : 4.770 18.192 585 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 6.59 % Allowed : 17.80 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.003 PHE W 94 TYR 0.003 0.001 TYR C 39 *********************** 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 95 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.446 Fit side-chains REVERT: A 72 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8853 (m) REVERT: E 50 GLN cc_start: 0.8221 (tp40) cc_final: 0.6971 (pt0) REVERT: W 45 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7006 (mtpp) REVERT: W 50 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6461 (tm130) REVERT: V 45 LYS cc_start: 0.7725 (mtmt) cc_final: 0.6990 (mtpp) REVERT: V 50 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7550 (tp40) REVERT: X 45 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7187 (mtpp) REVERT: X 50 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7641 (tp40) REVERT: X 83 GLU cc_start: 0.8081 (mp0) cc_final: 0.7612 (mp0) REVERT: Y 45 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7201 (mtpp) REVERT: Y 50 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7510 (tp40) REVERT: Y 83 GLU cc_start: 0.7825 (mp0) cc_final: 0.6986 (mp0) REVERT: Z 45 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7800 (mtpt) REVERT: Z 83 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7695 (mp0) outliers start: 27 outliers final: 19 residues processed: 83 average time/residue: 0.1447 time to fit residues: 15.8524 Evaluate side-chains 92 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 46 GLU 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 99 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 50 GLN Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 92 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 Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 29 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.4712 r_free = 0.4712 target = 0.186024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.163647 restraints weight = 4749.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.167138 restraints weight = 1913.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.169399 restraints weight = 1090.580| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2606 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= 0.279 Angle : 0.498 6.452 5465 Z= 0.281 Chirality : 0.054 0.136 725 Planarity : 0.002 0.015 685 Dihedral : 4.708 17.868 585 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 7.07 % Allowed : 17.56 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE W 94 TYR 0.003 0.001 TYR C 39 *********************** 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 97 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.453 Fit side-chains REVERT: A 72 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8860 (m) REVERT: E 50 GLN cc_start: 0.8219 (tp40) cc_final: 0.6956 (pt0) REVERT: W 45 LYS cc_start: 0.7800 (mtmt) cc_final: 0.6973 (mtpp) REVERT: W 50 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.6464 (tm130) REVERT: V 45 LYS cc_start: 0.7657 (mtmt) cc_final: 0.6938 (mtpp) REVERT: V 50 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7510 (tp40) REVERT: X 45 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7157 (mtpp) REVERT: X 50 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7520 (tp40) REVERT: X 83 GLU cc_start: 0.8074 (mp0) cc_final: 0.7602 (mp0) REVERT: Y 45 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7158 (mtpp) REVERT: Y 50 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7594 (tp40) REVERT: Y 83 GLU cc_start: 0.7797 (mp0) cc_final: 0.6943 (mp0) REVERT: Z 45 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7786 (mtpt) REVERT: Z 83 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7700 (mp0) outliers start: 29 outliers final: 21 residues processed: 84 average time/residue: 0.1391 time to fit residues: 15.0020 Evaluate side-chains 95 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 46 GLU 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 48 VAL 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 50 GLN Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 92 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 Z residue 62 GLN Chi-restraints excluded: chain Z residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 40.0000 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.4704 r_free = 0.4704 target = 0.185754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.163409 restraints weight = 4729.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.166900 restraints weight = 1915.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.169234 restraints weight = 1089.997| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 4045 Z= 0.311 Angle : 0.511 6.878 5465 Z= 0.290 Chirality : 0.055 0.138 725 Planarity : 0.002 0.010 685 Dihedral : 4.752 17.754 585 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 7.07 % Allowed : 17.32 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (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 PHE 0.024 0.003 PHE W 94 TYR 0.002 0.001 TYR C 39 ********************** 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 97 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.416 Fit side-chains REVERT: A 72 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8862 (m) REVERT: E 50 GLN cc_start: 0.8223 (tp40) cc_final: 0.6965 (pt0) REVERT: W 45 LYS cc_start: 0.7822 (mtmt) cc_final: 0.6988 (mtpp) REVERT: W 50 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.6479 (tm130) REVERT: V 45 LYS cc_start: 0.7669 (mtmt) cc_final: 0.6908 (mtpp) REVERT: V 50 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7523 (tp40) REVERT: X 45 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7200 (mtpp) REVERT: X 50 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: X 83 GLU cc_start: 0.8071 (mp0) cc_final: 0.7602 (mp0) REVERT: Y 45 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7175 (mtpp) REVERT: Y 50 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7610 (tp40) REVERT: Y 83 GLU cc_start: 0.7789 (mp0) cc_final: 0.6941 (mp0) REVERT: Z 45 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7788 (mtpt) REVERT: Z 83 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7703 (mp0) outliers start: 29 outliers final: 22 residues processed: 83 average time/residue: 0.1361 time to fit residues: 14.6745 Evaluate side-chains 96 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 65 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 46 GLU 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 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 50 GLN Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 92 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 62 GLN Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.4679 r_free = 0.4679 target = 0.183321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.160979 restraints weight = 4699.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.164352 restraints weight = 1896.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.166671 restraints weight = 1090.089| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 4045 Z= 0.411 Angle : 0.555 6.380 5465 Z= 0.317 Chirality : 0.056 0.142 725 Planarity : 0.002 0.015 685 Dihedral : 5.032 18.358 585 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 7.07 % Allowed : 17.32 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.004 PHE W 94 TYR 0.003 0.001 TYR B 39 =============================================================================== Job complete usr+sys time: 1225.19 seconds wall clock time: 23 minutes 17.40 seconds (1397.40 seconds total)