Starting phenix.real_space_refine on Wed Mar 5 22:15:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pes_20331/03_2025/6pes_20331.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pes_20331/03_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_20331/03_2025/6pes_20331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pes_20331/03_2025/6pes_20331.map" model { file = "/net/cci-nas-00/data/ceres_data/6pes_20331/03_2025/6pes_20331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pes_20331/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 1.85, per 1000 atoms: 0.46 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: 1.03 Conformation dependent library (CDL) restraints added in 578.0 milliseconds 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 64.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 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: 1.02 Time building geometry restraints manager: 1.23 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: 0.04 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: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.090 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- 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 : 0.729 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: 0.1973 time to fit residues: 19.0674 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 : 0.442 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 50.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.4706 r_free = 0.4706 target = 0.189660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.167804 restraints weight = 4695.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.171310 restraints weight = 1908.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.173686 restraints weight = 1074.457| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 4045 Z= 0.333 Angle : 0.515 3.413 5465 Z= 0.302 Chirality : 0.056 0.132 725 Planarity : 0.003 0.016 685 Dihedral : 5.046 16.436 585 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 5.85 % Allowed : 13.41 % 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: -1.91 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 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 108 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.403 Fit side-chains REVERT: A 72 THR cc_start: 0.9152 (m) cc_final: 0.8914 (m) REVERT: C 45 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7929 (mtpt) REVERT: C 99 GLN cc_start: 0.5574 (tt0) cc_final: 0.5230 (tt0) REVERT: D 80 LYS cc_start: 0.8618 (tttm) cc_final: 0.7174 (pttt) REVERT: E 50 GLN cc_start: 0.8244 (tp40) cc_final: 0.6768 (pm20) REVERT: W 45 LYS cc_start: 0.7515 (mtmt) cc_final: 0.6866 (mtpp) REVERT: W 83 GLU cc_start: 0.7810 (pm20) cc_final: 0.7417 (mp0) REVERT: V 45 LYS cc_start: 0.7667 (mtmt) cc_final: 0.6921 (mtpp) REVERT: V 83 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: X 45 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7284 (mtpp) REVERT: X 83 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: X 94 PHE cc_start: 0.7747 (t80) cc_final: 0.7471 (t80) REVERT: Y 45 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7076 (mtpp) REVERT: Y 83 GLU cc_start: 0.7919 (pm20) cc_final: 0.7430 (mp0) REVERT: Z 45 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7428 (mtpp) REVERT: Z 83 GLU cc_start: 0.7942 (pm20) cc_final: 0.7703 (mp0) outliers start: 24 outliers final: 16 residues processed: 92 average time/residue: 0.1460 time to fit residues: 16.9131 Evaluate side-chains 95 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 10.0000 chunk 16 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 0.0030 chunk 14 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 overall best weight: 6.3998 ------------------------------------------------------------------------------- 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 = 0.4722 r_free = 0.4722 target = 0.190344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.168570 restraints weight = 4629.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.172121 restraints weight = 1875.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.174442 restraints weight = 1047.323| |-----------------------------------------------------------------------------| r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 4045 Z= 0.275 Angle : 0.487 7.995 5465 Z= 0.277 Chirality : 0.055 0.126 725 Planarity : 0.002 0.013 685 Dihedral : 4.798 15.141 585 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 7.07 % Allowed : 15.37 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.99 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE W 94 TYR 0.004 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 107 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.392 Fit side-chains REVERT: A 72 THR cc_start: 0.9155 (m) cc_final: 0.8823 (m) REVERT: C 45 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7760 (mtpt) REVERT: D 80 LYS cc_start: 0.8601 (tttm) cc_final: 0.7209 (pttt) REVERT: E 50 GLN cc_start: 0.8230 (tp40) cc_final: 0.6929 (pt0) REVERT: E 66 VAL cc_start: 0.9097 (t) cc_final: 0.8819 (m) REVERT: W 45 LYS cc_start: 0.7616 (mtmt) cc_final: 0.7025 (mtpp) REVERT: W 81 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8017 (m) REVERT: V 45 LYS cc_start: 0.7696 (mtmt) cc_final: 0.6986 (mtpp) REVERT: V 83 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: X 45 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7399 (mtpp) REVERT: X 83 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: Y 45 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7093 (mtpp) REVERT: Y 83 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: Z 45 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7496 (mtpp) REVERT: Z 83 GLU cc_start: 0.7879 (pm20) cc_final: 0.7591 (mp0) outliers start: 29 outliers final: 23 residues processed: 87 average time/residue: 0.1501 time to fit residues: 16.6419 Evaluate side-chains 103 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 48 VAL 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 54 THR 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: 0.0040 chunk 26 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 overall best weight: 11.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 99 GLN D 99 GLN E 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.184457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.162666 restraints weight = 4779.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.166063 restraints weight = 1924.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.168068 restraints weight = 1087.438| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 4045 Z= 0.466 Angle : 0.571 5.757 5465 Z= 0.330 Chirality : 0.057 0.134 725 Planarity : 0.003 0.012 685 Dihedral : 5.227 17.798 585 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 8.78 % Allowed : 14.15 % Favored : 77.07 % 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: -2.42 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (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 C 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 112 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.397 Fit side-chains REVERT: E 50 GLN cc_start: 0.8339 (tp40) cc_final: 0.7025 (pt0) REVERT: W 45 LYS cc_start: 0.7648 (mtmt) cc_final: 0.6996 (mtpp) REVERT: W 50 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6466 (tm130) REVERT: V 45 LYS cc_start: 0.7720 (mtmt) cc_final: 0.6970 (mtpp) REVERT: X 45 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7366 (mtpp) REVERT: X 83 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: Y 45 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7106 (mtpp) REVERT: Y 50 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7880 (tp40) REVERT: Y 83 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: Z 45 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7596 (mtpp) REVERT: Z 83 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7881 (mp0) outliers start: 36 outliers final: 22 residues processed: 92 average time/residue: 0.1502 time to fit residues: 17.5460 Evaluate side-chains 101 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 54 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain X residue 83 GLU 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 Y residue 83 GLU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR 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: 50.0000 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.188123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.166416 restraints weight = 4779.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.169898 restraints weight = 1928.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.172212 restraints weight = 1081.398| |-----------------------------------------------------------------------------| r_work (final): 0.4539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2268 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= 0.272 Angle : 0.487 6.682 5465 Z= 0.277 Chirality : 0.055 0.143 725 Planarity : 0.002 0.010 685 Dihedral : 4.730 16.805 585 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 8.29 % Allowed : 14.39 % 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: -2.44 (0.31), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (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 108 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.432 Fit side-chains REVERT: A 72 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8814 (m) REVERT: E 50 GLN cc_start: 0.8258 (tp40) cc_final: 0.6964 (pt0) REVERT: W 45 LYS cc_start: 0.7716 (mtmt) cc_final: 0.7042 (mtpp) REVERT: W 50 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.6478 (tm130) REVERT: V 45 LYS cc_start: 0.7728 (mtmt) cc_final: 0.6992 (mtpp) REVERT: V 50 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7525 (tp40) REVERT: X 45 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7275 (mtpp) REVERT: X 50 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7787 (tp40) REVERT: X 83 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: Y 45 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7129 (mtpp) REVERT: Y 83 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: Z 45 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7557 (mtpp) REVERT: Z 83 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7770 (mp0) outliers start: 34 outliers final: 22 residues processed: 89 average time/residue: 0.1545 time to fit residues: 17.3327 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 : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 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 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 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 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.185796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.163321 restraints weight = 4763.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.166782 restraints weight = 1901.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.169120 restraints weight = 1080.547| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 4045 Z= 0.334 Angle : 0.510 6.107 5465 Z= 0.292 Chirality : 0.055 0.134 725 Planarity : 0.002 0.009 685 Dihedral : 4.845 18.548 585 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 8.05 % Allowed : 15.61 % Favored : 76.34 % 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: -2.60 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.003 PHE W 94 TYR 0.002 0.001 TYR C 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 105 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 0.436 Fit side-chains REVERT: A 72 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8846 (m) REVERT: B 45 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7987 (mtpt) REVERT: E 50 GLN cc_start: 0.8265 (tp40) cc_final: 0.6995 (pt0) REVERT: W 45 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7018 (mtpp) REVERT: W 50 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.6477 (tm130) REVERT: V 45 LYS cc_start: 0.7718 (mtmt) cc_final: 0.6977 (mtpp) REVERT: V 50 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7517 (tp40) REVERT: X 45 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7313 (mtpp) REVERT: X 50 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7731 (tp40) REVERT: X 83 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: Y 45 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7115 (mtpp) REVERT: Y 50 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7537 (tp40) REVERT: Y 83 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: Z 45 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7575 (mtpp) REVERT: Z 50 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8016 (tp40) REVERT: Z 83 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7746 (mp0) outliers start: 33 outliers final: 21 residues processed: 87 average time/residue: 0.1556 time to fit residues: 16.9980 Evaluate side-chains 100 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 X residue 83 GLU 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 Y residue 83 GLU Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR 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: 20.0000 chunk 10 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 overall best weight: 13.7996 ------------------------------------------------------------------------------- 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 = 0.4644 r_free = 0.4644 target = 0.181186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.158807 restraints weight = 4807.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.162163 restraints weight = 1950.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.164434 restraints weight = 1115.398| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 4045 Z= 0.559 Angle : 0.626 4.824 5465 Z= 0.364 Chirality : 0.058 0.141 725 Planarity : 0.003 0.011 685 Dihedral : 5.380 19.998 585 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 8.54 % Allowed : 14.63 % 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: -2.90 (0.29), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.004 PHE W 94 TYR 0.003 0.001 TYR B 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 109 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.444 Fit side-chains REVERT: E 50 GLN cc_start: 0.8286 (tp40) cc_final: 0.7036 (pt0) REVERT: E 99 GLN cc_start: 0.3273 (OUTLIER) cc_final: 0.2468 (pt0) REVERT: W 45 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7151 (mtpp) REVERT: W 50 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.6584 (tm130) REVERT: V 45 LYS cc_start: 0.7753 (mtmt) cc_final: 0.6987 (mtpp) REVERT: V 50 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7664 (tp40) REVERT: X 45 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7266 (mtpp) REVERT: X 50 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7789 (tp40) REVERT: Y 45 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7194 (mtpp) REVERT: Y 50 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7626 (tp40) REVERT: Z 45 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7805 (mtpt) REVERT: Z 50 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8063 (tp40) REVERT: Z 83 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7902 (mp0) outliers start: 35 outliers final: 25 residues processed: 89 average time/residue: 0.1538 time to fit residues: 17.1625 Evaluate side-chains 103 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN 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 Y residue 81 THR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 81 THR 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: 10.0000 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 40 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.188985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.166774 restraints weight = 4617.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.170248 restraints weight = 1859.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.172567 restraints weight = 1058.325| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4045 Z= 0.178 Angle : 0.455 5.763 5465 Z= 0.261 Chirality : 0.054 0.139 725 Planarity : 0.002 0.009 685 Dihedral : 4.482 18.582 585 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 6.34 % Allowed : 17.80 % Favored : 75.85 % 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: -2.73 (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 0.021 0.003 PHE W 94 TYR 0.002 0.001 TYR A 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 98 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.429 Fit side-chains REVERT: A 72 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8787 (m) REVERT: E 50 GLN cc_start: 0.8230 (tp40) cc_final: 0.6786 (pm20) REVERT: W 50 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.6506 (tm130) REVERT: V 45 LYS cc_start: 0.7682 (mtmt) cc_final: 0.6895 (mtpp) REVERT: V 50 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7539 (tp40) REVERT: X 45 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7145 (mtpp) REVERT: X 50 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7689 (tp40) REVERT: X 83 GLU cc_start: 0.8032 (mp0) cc_final: 0.7752 (mp0) REVERT: Y 45 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7127 (mtpp) REVERT: Y 50 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.5964 (tm130) REVERT: Y 83 GLU cc_start: 0.7975 (mp0) cc_final: 0.7666 (mp0) REVERT: Z 45 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7721 (mtpt) REVERT: Z 50 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7895 (tp40) REVERT: Z 83 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7507 (mp0) outliers start: 26 outliers final: 14 residues processed: 86 average time/residue: 0.1271 time to fit residues: 14.2735 Evaluate side-chains 91 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain W residue 50 GLN 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 50 GLN 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: 10.0000 chunk 42 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 20 optimal weight: 0.0670 chunk 6 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 0.0050 chunk 30 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 overall best weight: 6.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.187603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.165157 restraints weight = 4707.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.168629 restraints weight = 1892.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.170992 restraints weight = 1076.577| |-----------------------------------------------------------------------------| r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4045 Z= 0.257 Angle : 0.489 9.785 5465 Z= 0.273 Chirality : 0.054 0.136 725 Planarity : 0.002 0.010 685 Dihedral : 4.587 17.837 585 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.88 % Allowed : 19.27 % Favored : 75.85 % 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: -2.70 (0.30), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.003 PHE W 94 TYR 0.002 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 89 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.417 Fit side-chains REVERT: A 72 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8842 (m) REVERT: E 50 GLN cc_start: 0.8245 (tp40) cc_final: 0.6869 (pt0) REVERT: W 45 LYS cc_start: 0.7718 (mtmt) cc_final: 0.6874 (mtpp) REVERT: W 50 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6407 (tm130) REVERT: V 45 LYS cc_start: 0.7635 (mtmt) cc_final: 0.6846 (mtpp) REVERT: V 50 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7426 (tp40) REVERT: X 45 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7070 (mtpp) REVERT: X 50 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7423 (tp40) REVERT: X 83 GLU cc_start: 0.7957 (mp0) cc_final: 0.7623 (mp0) REVERT: Y 45 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7079 (mtpp) REVERT: Y 50 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7492 (tp40) REVERT: Y 83 GLU cc_start: 0.7978 (mp0) cc_final: 0.7333 (mp0) REVERT: Z 45 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7686 (mtpt) REVERT: Z 50 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7912 (tp40) REVERT: Z 83 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7677 (mp0) outliers start: 20 outliers final: 13 residues processed: 79 average time/residue: 0.1622 time to fit residues: 16.3219 Evaluate side-chains 90 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C 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 87 SER Chi-restraints excluded: chain W residue 50 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain X residue 50 GLN Chi-restraints excluded: chain X residue 81 THR Chi-restraints excluded: chain Y residue 50 GLN Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Z residue 50 GLN 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 40 optimal weight: 40.0000 chunk 32 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 53 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 42 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.185089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.162640 restraints weight = 4728.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.166053 restraints weight = 1909.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.168263 restraints weight = 1088.240| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 4045 Z= 0.341 Angle : 0.527 9.393 5465 Z= 0.296 Chirality : 0.055 0.137 725 Planarity : 0.002 0.016 685 Dihedral : 4.786 17.671 585 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.61 % Allowed : 18.29 % Favored : 76.10 % 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 0.024 0.003 PHE W 94 TYR 0.002 0.001 TYR B 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 95 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.395 Fit side-chains REVERT: A 72 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8824 (m) REVERT: E 50 GLN cc_start: 0.8248 (tp40) cc_final: 0.6986 (pt0) REVERT: E 99 GLN cc_start: 0.3425 (OUTLIER) cc_final: 0.2706 (pt0) REVERT: W 45 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7031 (mtpp) REVERT: W 50 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.6473 (tm130) REVERT: V 45 LYS cc_start: 0.7733 (mtmt) cc_final: 0.6979 (mtpp) REVERT: V 50 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7631 (tp40) REVERT: X 45 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7213 (mtpp) REVERT: X 50 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7774 (tp40) REVERT: Y 45 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7199 (mtpp) REVERT: Y 50 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7623 (tp40) REVERT: Y 83 GLU cc_start: 0.7950 (mp0) cc_final: 0.7586 (mp0) REVERT: Z 45 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7761 (mtpt) REVERT: Z 50 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8053 (tp40) REVERT: Z 83 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7766 (mp0) outliers start: 23 outliers final: 15 residues processed: 84 average time/residue: 0.1487 time to fit residues: 15.7692 Evaluate side-chains 93 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 48 VAL 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 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain W residue 50 GLN 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 50 GLN 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: 20.0000 chunk 23 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 21 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.184456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.162106 restraints weight = 4673.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.165521 restraints weight = 1880.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.167854 restraints weight = 1076.475| |-----------------------------------------------------------------------------| r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2640 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= 0.372 Angle : 0.551 9.222 5465 Z= 0.309 Chirality : 0.055 0.139 725 Planarity : 0.002 0.015 685 Dihedral : 4.885 17.632 585 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 6.10 % Allowed : 17.56 % Favored : 76.34 % 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 : -2.16 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.004 PHE W 94 TYR 0.002 0.001 TYR B 39 =============================================================================== Job complete usr+sys time: 1270.53 seconds wall clock time: 23 minutes 18.59 seconds (1398.59 seconds total)