Starting phenix.real_space_refine on Sun Aug 24 00:27:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkq_41357/08_2025/8tkq_41357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkq_41357/08_2025/8tkq_41357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tkq_41357/08_2025/8tkq_41357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkq_41357/08_2025/8tkq_41357.map" model { file = "/net/cci-nas-00/data/ceres_data/8tkq_41357/08_2025/8tkq_41357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkq_41357/08_2025/8tkq_41357.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 9977 2.51 5 N 2871 2.21 5 O 3014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15950 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "B" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "C" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "D" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "E" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "F" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "G" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "I" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "J" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "K" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Time building chain proxies: 3.45, per 1000 atoms: 0.22 Number of scatterers: 15950 At special positions: 0 Unit cell: (132.08, 133.731, 77.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3014 8.00 N 2871 7.00 C 9977 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: 1.15 Conformation dependent library (CDL) restraints added in 681.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3674 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 24 sheets defined 43.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.735A pdb=" N ARG A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 134 through 157 removed outlier: 4.140A pdb=" N SER A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 6.375A pdb=" N ALA A 161 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.692A pdb=" N LYS A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'B' and resid 32 through 45 removed outlier: 3.766A pdb=" N ARG B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 80 Processing helix chain 'B' and resid 134 through 156 removed outlier: 3.607A pdb=" N VAL B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 163 removed outlier: 7.082A pdb=" N ASN B 160 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA B 161 " --> pdb=" O PHE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 197 through 207 Processing helix chain 'C' and resid 32 through 45 removed outlier: 3.739A pdb=" N ARG C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 80 Processing helix chain 'C' and resid 134 through 157 removed outlier: 4.144A pdb=" N SER C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 removed outlier: 6.430A pdb=" N ALA C 161 " --> pdb=" O PHE C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.786A pdb=" N ARG D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 Processing helix chain 'D' and resid 134 through 157 removed outlier: 4.085A pdb=" N SER D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 removed outlier: 6.336A pdb=" N ALA D 161 " --> pdb=" O PHE D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 197 through 206 removed outlier: 3.552A pdb=" N ASN D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 45 removed outlier: 3.704A pdb=" N ARG E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 Processing helix chain 'E' and resid 67 through 80 Processing helix chain 'E' and resid 134 through 157 removed outlier: 4.004A pdb=" N SER E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 removed outlier: 6.330A pdb=" N ALA E 161 " --> pdb=" O PHE E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 Processing helix chain 'E' and resid 197 through 208 removed outlier: 3.554A pdb=" N CYS E 208 " --> pdb=" O ARG E 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 45 removed outlier: 3.698A pdb=" N ARG F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 Processing helix chain 'F' and resid 134 through 157 removed outlier: 3.980A pdb=" N SER F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 163 removed outlier: 6.407A pdb=" N ALA F 161 " --> pdb=" O PHE F 158 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 162 " --> pdb=" O GLY F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 removed outlier: 3.509A pdb=" N LYS F 177 " --> pdb=" O ARG F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 207 Processing helix chain 'G' and resid 32 through 44 removed outlier: 3.743A pdb=" N ARG G 44 " --> pdb=" O GLN G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 80 Processing helix chain 'G' and resid 134 through 157 removed outlier: 4.001A pdb=" N SER G 157 " --> pdb=" O ARG G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 163 removed outlier: 6.271A pdb=" N ALA G 161 " --> pdb=" O PHE G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 167 Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'H' and resid 32 through 44 removed outlier: 3.791A pdb=" N ARG H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 80 Processing helix chain 'H' and resid 134 through 157 removed outlier: 4.105A pdb=" N SER H 157 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 163 removed outlier: 6.262A pdb=" N ALA H 161 " --> pdb=" O PHE H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 177 removed outlier: 3.585A pdb=" N LYS H 177 " --> pdb=" O ARG H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 207 Processing helix chain 'I' and resid 32 through 45 removed outlier: 3.763A pdb=" N ARG I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.557A pdb=" N ILE I 52 " --> pdb=" O PRO I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 80 Processing helix chain 'I' and resid 134 through 157 removed outlier: 4.058A pdb=" N SER I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 163 removed outlier: 6.417A pdb=" N ALA I 161 " --> pdb=" O PHE I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 177 removed outlier: 3.518A pdb=" N LYS I 177 " --> pdb=" O ARG I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 207 Processing helix chain 'J' and resid 32 through 45 removed outlier: 3.707A pdb=" N ARG J 44 " --> pdb=" O GLN J 40 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN J 45 " --> pdb=" O LYS J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 79 Processing helix chain 'J' and resid 134 through 157 removed outlier: 3.546A pdb=" N VAL J 147 " --> pdb=" O ARG J 143 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER J 157 " --> pdb=" O ARG J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 163 removed outlier: 6.269A pdb=" N ALA J 161 " --> pdb=" O PHE J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 176 Processing helix chain 'J' and resid 197 through 206 removed outlier: 3.659A pdb=" N ASN J 206 " --> pdb=" O GLU J 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 45 removed outlier: 3.706A pdb=" N ARG K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN K 45 " --> pdb=" O LYS K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 52 removed outlier: 3.512A pdb=" N TYR K 51 " --> pdb=" O GLY K 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE K 52 " --> pdb=" O PRO K 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 52' Processing helix chain 'K' and resid 67 through 80 Processing helix chain 'K' and resid 134 through 157 removed outlier: 3.946A pdb=" N SER K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 163 removed outlier: 6.189A pdb=" N ALA K 161 " --> pdb=" O PHE K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 177 Processing helix chain 'K' and resid 197 through 207 removed outlier: 3.649A pdb=" N ASN K 206 " --> pdb=" O GLU K 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 99 removed outlier: 8.008A pdb=" N SER A 87 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN A 114 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 89 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ARG A 112 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLN A 91 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 110 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL A 93 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS A 108 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 99 removed outlier: 5.326A pdb=" N HIS B 86 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN B 114 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG B 112 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 90 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY B 106 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 96 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR B 104 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 98 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 99 removed outlier: 7.984A pdb=" N SER C 87 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLN C 114 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR C 89 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ARG C 112 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLN C 91 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE C 110 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL C 93 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS C 108 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 56 removed outlier: 3.615A pdb=" N TYR D 65 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 84 through 90 removed outlier: 6.780A pdb=" N PHE D 110 " --> pdb=" O THR D 89 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS D 108 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL D 93 " --> pdb=" O CYS D 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 84 through 90 removed outlier: 6.780A pdb=" N PHE D 110 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'E' and resid 84 through 90 removed outlier: 6.815A pdb=" N PHE E 110 " --> pdb=" O THR E 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS E 108 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL E 93 " --> pdb=" O CYS E 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 84 through 90 removed outlier: 6.815A pdb=" N PHE E 110 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 99 removed outlier: 5.410A pdb=" N HIS F 86 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN F 114 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE F 88 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG F 112 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F 90 " --> pdb=" O PHE F 110 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY F 106 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL F 96 " --> pdb=" O TYR F 104 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR F 104 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU F 98 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'G' and resid 84 through 99 removed outlier: 5.409A pdb=" N HIS G 86 " --> pdb=" O GLN G 114 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLN G 114 " --> pdb=" O HIS G 86 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE G 88 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG G 112 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN G 90 " --> pdb=" O PHE G 110 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY G 106 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL G 96 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR G 104 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU G 98 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'H' and resid 84 through 99 removed outlier: 8.036A pdb=" N SER H 87 " --> pdb=" O GLN H 114 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLN H 114 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR H 89 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ARG H 112 " --> pdb=" O THR H 89 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN H 91 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE H 110 " --> pdb=" O GLN H 91 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL H 93 " --> pdb=" O CYS H 108 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS H 108 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 56 Processing sheet with id=AC2, first strand: chain 'I' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS I 86 " --> pdb=" O GLN I 114 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN I 114 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE I 88 " --> pdb=" O ARG I 112 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG I 112 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN I 90 " --> pdb=" O PHE I 110 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY I 106 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL I 96 " --> pdb=" O TYR I 104 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR I 104 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU I 98 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS I 102 " --> pdb=" O LEU I 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 52 through 56 Processing sheet with id=AC4, first strand: chain 'J' and resid 84 through 99 removed outlier: 5.394A pdb=" N HIS J 86 " --> pdb=" O GLN J 114 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLN J 114 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE J 88 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG J 112 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN J 90 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY J 106 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL J 96 " --> pdb=" O TYR J 104 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR J 104 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU J 98 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYS J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 53 through 56 Processing sheet with id=AC6, first strand: chain 'K' and resid 84 through 99 removed outlier: 5.374A pdb=" N HIS K 86 " --> pdb=" O GLN K 114 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLN K 114 " --> pdb=" O HIS K 86 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE K 88 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG K 112 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN K 90 " --> pdb=" O PHE K 110 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY K 106 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL K 96 " --> pdb=" O TYR K 104 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR K 104 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU K 98 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2250 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: 1.98 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5445 1.34 - 1.46: 2750 1.46 - 1.57: 7909 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 16214 Sorted by residual: bond pdb=" CA GLY I 83 " pdb=" C GLY I 83 " ideal model delta sigma weight residual 1.514 1.496 0.018 1.41e-02 5.03e+03 1.62e+00 bond pdb=" CA GLY J 125 " pdb=" C GLY J 125 " ideal model delta sigma weight residual 1.516 1.506 0.010 8.20e-03 1.49e+04 1.59e+00 bond pdb=" CA GLY K 83 " pdb=" C GLY K 83 " ideal model delta sigma weight residual 1.514 1.497 0.017 1.41e-02 5.03e+03 1.44e+00 bond pdb=" N GLN K 28 " pdb=" CA GLN K 28 " ideal model delta sigma weight residual 1.458 1.446 0.012 1.08e-02 8.57e+03 1.25e+00 bond pdb=" CG GLN E 91 " pdb=" CD GLN E 91 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.14e+00 ... (remaining 16209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 21143 1.64 - 3.27: 584 3.27 - 4.91: 43 4.91 - 6.54: 13 6.54 - 8.18: 8 Bond angle restraints: 21791 Sorted by residual: angle pdb=" C GLY I 131 " pdb=" N LEU I 132 " pdb=" CA LEU I 132 " ideal model delta sigma weight residual 121.31 129.49 -8.18 1.49e+00 4.50e-01 3.01e+01 angle pdb=" C GLY H 131 " pdb=" N LEU H 132 " pdb=" CA LEU H 132 " ideal model delta sigma weight residual 121.31 129.35 -8.04 1.49e+00 4.50e-01 2.91e+01 angle pdb=" C GLY E 131 " pdb=" N LEU E 132 " pdb=" CA LEU E 132 " ideal model delta sigma weight residual 121.31 128.67 -7.36 1.49e+00 4.50e-01 2.44e+01 angle pdb=" N LEU E 132 " pdb=" CA LEU E 132 " pdb=" C LEU E 132 " ideal model delta sigma weight residual 110.35 116.36 -6.01 1.40e+00 5.10e-01 1.84e+01 angle pdb=" N LEU I 132 " pdb=" CA LEU I 132 " pdb=" C LEU I 132 " ideal model delta sigma weight residual 110.35 116.10 -5.75 1.40e+00 5.10e-01 1.69e+01 ... (remaining 21786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 8787 16.30 - 32.61: 817 32.61 - 48.91: 136 48.91 - 65.21: 37 65.21 - 81.52: 24 Dihedral angle restraints: 9801 sinusoidal: 4004 harmonic: 5797 Sorted by residual: dihedral pdb=" CA GLY I 131 " pdb=" C GLY I 131 " pdb=" N LEU I 132 " pdb=" CA LEU I 132 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLY F 131 " pdb=" C GLY F 131 " pdb=" N LEU F 132 " pdb=" CA LEU F 132 " ideal model delta harmonic sigma weight residual 180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLY D 131 " pdb=" C GLY D 131 " pdb=" N LEU D 132 " pdb=" CA LEU D 132 " ideal model delta harmonic sigma weight residual -180.00 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 9798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1191 0.030 - 0.061: 752 0.061 - 0.091: 243 0.091 - 0.122: 93 0.122 - 0.152: 20 Chirality restraints: 2299 Sorted by residual: chirality pdb=" CA PRO F 198 " pdb=" N PRO F 198 " pdb=" C PRO F 198 " pdb=" CB PRO F 198 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA PRO I 198 " pdb=" N PRO I 198 " pdb=" C PRO I 198 " pdb=" CB PRO I 198 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA PRO A 198 " pdb=" N PRO A 198 " pdb=" C PRO A 198 " pdb=" CB PRO A 198 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 2296 not shown) Planarity restraints: 2882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 197 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO G 198 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 198 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 198 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 86 " 0.015 2.00e-02 2.50e+03 1.22e-02 2.23e+00 pdb=" CG HIS C 86 " -0.024 2.00e-02 2.50e+03 pdb=" ND1 HIS C 86 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS C 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 86 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS C 86 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 86 " 0.012 2.00e-02 2.50e+03 1.08e-02 1.76e+00 pdb=" CG HIS A 86 " -0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 86 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 86 " 0.003 2.00e-02 2.50e+03 ... (remaining 2879 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 512 2.71 - 3.26: 15163 3.26 - 3.81: 25617 3.81 - 4.35: 33257 4.35 - 4.90: 56606 Nonbonded interactions: 131155 Sorted by model distance: nonbonded pdb=" O LEU F 47 " pdb=" OH TYR F 171 " model vdw 2.166 3.040 nonbonded pdb=" O LEU H 47 " pdb=" OH TYR H 171 " model vdw 2.179 3.040 nonbonded pdb=" O LEU E 47 " pdb=" OH TYR E 171 " model vdw 2.189 3.040 nonbonded pdb=" O LEU J 47 " pdb=" OH TYR J 171 " model vdw 2.208 3.040 nonbonded pdb=" O LEU A 47 " pdb=" OH TYR A 171 " model vdw 2.226 3.040 ... (remaining 131150 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.090 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.007 0.032 16214 Z= 0.307 Angle : 0.660 8.179 21791 Z= 0.409 Chirality : 0.044 0.152 2299 Planarity : 0.003 0.042 2882 Dihedral : 13.507 81.516 6127 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2002 helix: -0.14 (0.17), residues: 748 sheet: -0.53 (0.23), residues: 495 loop : -1.15 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 55 TYR 0.017 0.002 TYR J 171 PHE 0.016 0.002 PHE D 26 TRP 0.011 0.002 TRP H 84 HIS 0.009 0.002 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00679 (16214) covalent geometry : angle 0.66001 (21791) hydrogen bonds : bond 0.13465 ( 776) hydrogen bonds : angle 6.01994 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.597 Fit side-chains REVERT: A 132 LEU cc_start: 0.8390 (mp) cc_final: 0.8166 (mt) REVERT: B 100 ASN cc_start: 0.7659 (t0) cc_final: 0.7306 (t0) REVERT: C 46 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7346 (mtt-85) REVERT: C 62 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7723 (ttmm) REVERT: C 100 ASN cc_start: 0.7706 (t0) cc_final: 0.7367 (t0) REVERT: C 202 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6795 (tm-30) REVERT: D 81 TYR cc_start: 0.8703 (p90) cc_final: 0.8319 (p90) REVERT: D 190 LYS cc_start: 0.7615 (mtpp) cc_final: 0.7405 (mtpp) REVERT: D 202 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6840 (tm-30) REVERT: E 76 ASN cc_start: 0.8484 (m-40) cc_final: 0.8222 (m-40) REVERT: F 100 ASN cc_start: 0.7749 (t0) cc_final: 0.7464 (t0) REVERT: G 100 ASN cc_start: 0.7630 (t0) cc_final: 0.7315 (t0) REVERT: G 201 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6383 (mm-30) REVERT: H 100 ASN cc_start: 0.7777 (t0) cc_final: 0.7423 (t0) REVERT: H 202 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6402 (tm-30) REVERT: H 206 ASN cc_start: 0.7825 (m-40) cc_final: 0.7230 (m-40) REVERT: I 50 GLU cc_start: 0.7645 (mp0) cc_final: 0.7348 (mp0) REVERT: I 100 ASN cc_start: 0.7699 (t0) cc_final: 0.7392 (t0) REVERT: I 197 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6737 (mm-30) REVERT: J 100 ASN cc_start: 0.7618 (t0) cc_final: 0.7323 (t0) REVERT: J 202 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7312 (tm-30) REVERT: K 202 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7203 (tm-30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.7205 time to fit residues: 276.6681 Evaluate side-chains 339 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 45 GLN A 69 HIS A 86 HIS A 100 ASN A 114 GLN B 37 GLN B 76 ASN B 86 HIS B 91 GLN C 28 GLN C 37 GLN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 HIS D 30 GLN D 37 GLN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN D 100 ASN D 176 ASN E 37 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN F 37 GLN F 69 HIS F 86 HIS F 90 GLN F 164 ASN G 37 GLN G 40 GLN G 45 GLN G 86 HIS G 92 ASN G 114 GLN H 30 GLN H 37 GLN H 86 HIS H 92 ASN H 114 GLN I 30 GLN I 37 GLN I 40 GLN I 86 HIS I 121 HIS J 30 GLN J 37 GLN J 86 HIS J 90 GLN J 92 ASN J 121 HIS J 206 ASN K 30 GLN K 37 GLN K 76 ASN K 86 HIS K 91 GLN K 100 ASN K 114 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.148849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129990 restraints weight = 19813.046| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.76 r_work: 0.3680 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16214 Z= 0.153 Angle : 0.501 6.025 21791 Z= 0.273 Chirality : 0.041 0.141 2299 Planarity : 0.003 0.042 2882 Dihedral : 4.108 17.704 2255 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.66 % Allowed : 8.38 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.19), residues: 2002 helix: 1.24 (0.19), residues: 770 sheet: -0.06 (0.23), residues: 495 loop : -0.54 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 70 TYR 0.014 0.001 TYR E 36 PHE 0.010 0.001 PHE D 26 TRP 0.007 0.001 TRP H 84 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00347 (16214) covalent geometry : angle 0.50145 (21791) hydrogen bonds : bond 0.04099 ( 776) hydrogen bonds : angle 4.64663 ( 2250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 336 time to evaluate : 0.562 Fit side-chains REVERT: A 201 GLU cc_start: 0.7076 (mp0) cc_final: 0.6730 (mp0) REVERT: B 100 ASN cc_start: 0.8292 (t0) cc_final: 0.7980 (t0) REVERT: C 62 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7949 (ttmm) REVERT: C 197 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7341 (mt-10) REVERT: C 202 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7329 (tm-30) REVERT: D 81 TYR cc_start: 0.8775 (p90) cc_final: 0.8475 (p90) REVERT: D 190 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7699 (mtpp) REVERT: D 202 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7233 (tm-30) REVERT: E 76 ASN cc_start: 0.8506 (m-40) cc_final: 0.8287 (m-40) REVERT: F 100 ASN cc_start: 0.8503 (t0) cc_final: 0.8190 (t0) REVERT: G 100 ASN cc_start: 0.8295 (t0) cc_final: 0.7992 (t0) REVERT: H 100 ASN cc_start: 0.8381 (t0) cc_final: 0.8042 (t0) REVERT: H 197 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7296 (mt-10) REVERT: H 202 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7001 (tm-30) REVERT: H 206 ASN cc_start: 0.8137 (m-40) cc_final: 0.7717 (m-40) REVERT: I 204 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7157 (ttp80) REVERT: J 100 ASN cc_start: 0.8304 (t0) cc_final: 0.8010 (t0) REVERT: J 202 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7486 (tp30) REVERT: J 206 ASN cc_start: 0.8334 (m110) cc_final: 0.7944 (m110) REVERT: K 202 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7521 (tm-30) outliers start: 28 outliers final: 11 residues processed: 341 average time/residue: 0.6876 time to fit residues: 252.9773 Evaluate side-chains 340 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 329 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain I residue 206 ASN Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 190 optimal weight: 0.0050 chunk 144 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 10 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 125 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 121 HIS B 76 ASN B 121 HIS B 176 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 HIS D 176 ASN E 40 GLN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 90 GLN G 176 ASN J 90 GLN J 92 ASN K 37 GLN K 76 ASN K 181 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.151497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.132651 restraints weight = 19936.120| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.78 r_work: 0.3710 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16214 Z= 0.082 Angle : 0.435 5.390 21791 Z= 0.235 Chirality : 0.039 0.156 2299 Planarity : 0.003 0.035 2882 Dihedral : 3.765 16.751 2255 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.84 % Allowed : 10.16 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.19), residues: 2002 helix: 1.86 (0.19), residues: 770 sheet: 0.31 (0.24), residues: 495 loop : -0.07 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 193 TYR 0.010 0.001 TYR E 36 PHE 0.008 0.001 PHE D 26 TRP 0.004 0.001 TRP F 84 HIS 0.002 0.001 HIS G 86 Details of bonding type rmsd covalent geometry : bond 0.00177 (16214) covalent geometry : angle 0.43473 (21791) hydrogen bonds : bond 0.02960 ( 776) hydrogen bonds : angle 4.19796 ( 2250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 302 time to evaluate : 0.609 Fit side-chains REVERT: A 201 GLU cc_start: 0.7193 (mp0) cc_final: 0.6855 (mp0) REVERT: B 77 GLU cc_start: 0.7986 (mp0) cc_final: 0.7400 (mp0) REVERT: B 100 ASN cc_start: 0.8194 (t0) cc_final: 0.7881 (t0) REVERT: C 202 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7352 (tm-30) REVERT: D 81 TYR cc_start: 0.8755 (p90) cc_final: 0.8441 (p90) REVERT: D 132 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7828 (mt) REVERT: D 190 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7741 (mtpp) REVERT: D 202 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7039 (tm-30) REVERT: D 206 ASN cc_start: 0.8149 (m-40) cc_final: 0.7789 (m-40) REVERT: E 78 MET cc_start: 0.8511 (tpp) cc_final: 0.8242 (tpt) REVERT: E 197 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7033 (mm-30) REVERT: E 201 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: G 77 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: G 100 ASN cc_start: 0.8300 (t0) cc_final: 0.8006 (t0) REVERT: H 67 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7220 (mt-10) REVERT: H 100 ASN cc_start: 0.8373 (t0) cc_final: 0.8018 (t0) REVERT: H 202 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7028 (tm-30) REVERT: J 100 ASN cc_start: 0.8261 (t0) cc_final: 0.7968 (t0) REVERT: J 133 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8274 (mtpp) REVERT: J 201 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: J 206 ASN cc_start: 0.8311 (m110) cc_final: 0.8106 (m-40) REVERT: K 202 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7433 (tm-30) outliers start: 31 outliers final: 14 residues processed: 310 average time/residue: 0.6861 time to fit residues: 229.9048 Evaluate side-chains 311 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 293 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 75 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 93 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 0.3980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN H 121 HIS J 76 ASN K 37 GLN K 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130897 restraints weight = 19874.123| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.76 r_work: 0.3687 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16214 Z= 0.129 Angle : 0.443 5.379 21791 Z= 0.241 Chirality : 0.040 0.135 2299 Planarity : 0.003 0.034 2882 Dihedral : 3.712 14.772 2255 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.72 % Allowed : 11.94 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.19), residues: 2002 helix: 2.09 (0.18), residues: 770 sheet: 0.47 (0.24), residues: 495 loop : 0.24 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 193 TYR 0.010 0.001 TYR E 36 PHE 0.008 0.001 PHE D 26 TRP 0.007 0.001 TRP H 84 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00293 (16214) covalent geometry : angle 0.44316 (21791) hydrogen bonds : bond 0.03520 ( 776) hydrogen bonds : angle 4.15147 ( 2250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 311 time to evaluate : 0.453 Fit side-chains REVERT: A 201 GLU cc_start: 0.7350 (mp0) cc_final: 0.7116 (mp0) REVERT: B 77 GLU cc_start: 0.7984 (mp0) cc_final: 0.7426 (mp0) REVERT: B 100 ASN cc_start: 0.8181 (t0) cc_final: 0.7892 (t0) REVERT: C 202 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 81 TYR cc_start: 0.8784 (p90) cc_final: 0.8471 (p90) REVERT: D 132 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7908 (mt) REVERT: D 190 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7766 (mtpp) REVERT: D 202 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7262 (tm-30) REVERT: E 76 ASN cc_start: 0.8490 (m-40) cc_final: 0.8237 (m-40) REVERT: E 197 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7022 (mm-30) REVERT: E 201 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: F 46 ARG cc_start: 0.8402 (mtt90) cc_final: 0.8044 (mtt-85) REVERT: G 77 GLU cc_start: 0.7996 (mp0) cc_final: 0.7669 (mp0) REVERT: G 100 ASN cc_start: 0.8304 (t0) cc_final: 0.8015 (t0) REVERT: H 67 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7254 (mt-10) REVERT: H 100 ASN cc_start: 0.8384 (t0) cc_final: 0.8034 (t0) REVERT: I 56 MET cc_start: 0.7207 (mmm) cc_final: 0.6924 (tmm) REVERT: J 100 ASN cc_start: 0.8314 (t0) cc_final: 0.8018 (t0) REVERT: J 201 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: K 202 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7436 (tm-30) outliers start: 29 outliers final: 14 residues processed: 319 average time/residue: 0.7163 time to fit residues: 245.6455 Evaluate side-chains 323 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 306 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 181 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 156 optimal weight: 0.8980 chunk 68 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 167 optimal weight: 0.4980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN J 76 ASN K 37 GLN K 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.131573 restraints weight = 20049.736| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.71 r_work: 0.3701 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16214 Z= 0.094 Angle : 0.423 6.121 21791 Z= 0.228 Chirality : 0.039 0.130 2299 Planarity : 0.003 0.032 2882 Dihedral : 3.600 15.161 2255 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.02 % Allowed : 12.89 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.19), residues: 2002 helix: 2.35 (0.18), residues: 770 sheet: 0.64 (0.24), residues: 495 loop : 0.49 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 193 TYR 0.010 0.001 TYR E 171 PHE 0.006 0.001 PHE D 26 TRP 0.005 0.001 TRP H 84 HIS 0.004 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00211 (16214) covalent geometry : angle 0.42306 (21791) hydrogen bonds : bond 0.03012 ( 776) hydrogen bonds : angle 4.01875 ( 2250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 0.703 Fit side-chains REVERT: B 77 GLU cc_start: 0.8001 (mp0) cc_final: 0.7473 (mp0) REVERT: B 100 ASN cc_start: 0.8202 (t0) cc_final: 0.7914 (t0) REVERT: C 77 GLU cc_start: 0.8087 (mp0) cc_final: 0.7691 (mp0) REVERT: C 202 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7292 (tm-30) REVERT: D 81 TYR cc_start: 0.8767 (p90) cc_final: 0.8484 (p90) REVERT: D 190 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7762 (mtpp) REVERT: D 202 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7097 (tm-30) REVERT: D 206 ASN cc_start: 0.8126 (m-40) cc_final: 0.7684 (m-40) REVERT: E 76 ASN cc_start: 0.8443 (m-40) cc_final: 0.8196 (m-40) REVERT: E 197 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6964 (mm-30) REVERT: E 201 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: G 77 GLU cc_start: 0.7968 (mp0) cc_final: 0.7671 (mp0) REVERT: G 100 ASN cc_start: 0.8297 (t0) cc_final: 0.8007 (t0) REVERT: H 67 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7203 (mt-10) REVERT: H 202 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7047 (tm-30) REVERT: I 56 MET cc_start: 0.7179 (mmm) cc_final: 0.6923 (tmm) REVERT: J 100 ASN cc_start: 0.8283 (t0) cc_final: 0.7991 (t0) REVERT: J 201 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: K 202 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 34 outliers final: 21 residues processed: 304 average time/residue: 0.7220 time to fit residues: 236.6354 Evaluate side-chains 308 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 285 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 13 optimal weight: 0.0050 chunk 183 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 92 ASN G 76 ASN G 176 ASN J 76 ASN J 176 ASN K 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.148347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129086 restraints weight = 19867.022| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.76 r_work: 0.3668 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16214 Z= 0.133 Angle : 0.440 5.873 21791 Z= 0.240 Chirality : 0.040 0.138 2299 Planarity : 0.003 0.045 2882 Dihedral : 3.630 14.949 2255 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.38 % Allowed : 13.31 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.19), residues: 2002 helix: 2.41 (0.18), residues: 770 sheet: 0.76 (0.24), residues: 495 loop : 0.62 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 204 TYR 0.010 0.001 TYR E 171 PHE 0.008 0.001 PHE D 26 TRP 0.007 0.001 TRP H 84 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00305 (16214) covalent geometry : angle 0.44033 (21791) hydrogen bonds : bond 0.03497 ( 776) hydrogen bonds : angle 4.07185 ( 2250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 0.438 Fit side-chains REVERT: B 77 GLU cc_start: 0.8025 (mp0) cc_final: 0.7654 (mp0) REVERT: B 100 ASN cc_start: 0.8251 (t0) cc_final: 0.7976 (t0) REVERT: C 77 GLU cc_start: 0.8032 (mp0) cc_final: 0.7602 (mp0) REVERT: C 202 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7381 (tm-30) REVERT: D 81 TYR cc_start: 0.8740 (p90) cc_final: 0.8421 (p90) REVERT: D 190 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7867 (mtpp) REVERT: D 202 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7162 (tm-30) REVERT: D 206 ASN cc_start: 0.8152 (m-40) cc_final: 0.7707 (m-40) REVERT: E 76 ASN cc_start: 0.8502 (m-40) cc_final: 0.8264 (m-40) REVERT: E 197 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7073 (mm-30) REVERT: E 201 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: F 204 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7265 (ttp80) REVERT: G 100 ASN cc_start: 0.8408 (t0) cc_final: 0.8109 (t0) REVERT: H 62 LYS cc_start: 0.8372 (tttt) cc_final: 0.8135 (tttt) REVERT: H 67 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7211 (mt-10) REVERT: H 202 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7079 (tm-30) REVERT: I 56 MET cc_start: 0.7226 (mmm) cc_final: 0.6983 (tmm) REVERT: J 100 ASN cc_start: 0.8311 (t0) cc_final: 0.8022 (t0) REVERT: J 201 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: J 202 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7679 (tp30) REVERT: K 100 ASN cc_start: 0.8406 (t0) cc_final: 0.8064 (t0) REVERT: K 202 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7440 (tm-30) outliers start: 40 outliers final: 28 residues processed: 319 average time/residue: 0.7143 time to fit residues: 244.8676 Evaluate side-chains 330 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 300 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 196 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN J 76 ASN K 37 GLN K 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.148532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129420 restraints weight = 19887.730| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.76 r_work: 0.3676 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16214 Z= 0.109 Angle : 0.438 8.728 21791 Z= 0.237 Chirality : 0.039 0.159 2299 Planarity : 0.003 0.059 2882 Dihedral : 3.589 15.288 2255 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.14 % Allowed : 14.38 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.19), residues: 2002 helix: 2.50 (0.18), residues: 770 sheet: 0.85 (0.24), residues: 495 loop : 0.74 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 204 TYR 0.010 0.001 TYR E 171 PHE 0.006 0.001 PHE D 26 TRP 0.006 0.001 TRP H 84 HIS 0.004 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00249 (16214) covalent geometry : angle 0.43850 (21791) hydrogen bonds : bond 0.03219 ( 776) hydrogen bonds : angle 3.99727 ( 2250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 0.601 Fit side-chains REVERT: B 77 GLU cc_start: 0.8019 (mp0) cc_final: 0.7671 (mp0) REVERT: B 100 ASN cc_start: 0.8256 (t0) cc_final: 0.7985 (t0) REVERT: C 77 GLU cc_start: 0.8034 (mp0) cc_final: 0.7610 (mp0) REVERT: C 197 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7153 (mt-10) REVERT: C 202 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7381 (tm-30) REVERT: D 81 TYR cc_start: 0.8732 (p90) cc_final: 0.8434 (p90) REVERT: D 190 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7888 (mtpp) REVERT: D 202 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7159 (tm-30) REVERT: D 206 ASN cc_start: 0.8148 (m-40) cc_final: 0.7709 (m-40) REVERT: E 76 ASN cc_start: 0.8480 (m-40) cc_final: 0.8232 (m-40) REVERT: E 197 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7013 (mm-30) REVERT: E 201 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: F 204 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7249 (ttp80) REVERT: G 100 ASN cc_start: 0.8377 (t0) cc_final: 0.8086 (t0) REVERT: G 133 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8310 (mtpp) REVERT: H 62 LYS cc_start: 0.8381 (tttt) cc_final: 0.8142 (tttt) REVERT: H 67 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7184 (mt-10) REVERT: H 202 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7075 (tm-30) REVERT: I 56 MET cc_start: 0.7219 (mmm) cc_final: 0.6991 (tmm) REVERT: J 100 ASN cc_start: 0.8311 (t0) cc_final: 0.8027 (t0) REVERT: J 201 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: K 100 ASN cc_start: 0.8380 (t0) cc_final: 0.8051 (t0) REVERT: K 202 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7398 (tm-30) outliers start: 36 outliers final: 32 residues processed: 314 average time/residue: 0.7889 time to fit residues: 266.1589 Evaluate side-chains 332 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 298 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Chi-restraints excluded: chain K residue 132 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN H 91 GLN K 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126187 restraints weight = 20043.370| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.75 r_work: 0.3636 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 16214 Z= 0.290 Angle : 0.531 7.947 21791 Z= 0.290 Chirality : 0.044 0.163 2299 Planarity : 0.004 0.070 2882 Dihedral : 3.906 16.340 2255 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.26 % Allowed : 14.38 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.19), residues: 2002 helix: 2.16 (0.18), residues: 770 sheet: 0.75 (0.24), residues: 495 loop : 0.66 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 204 TYR 0.015 0.002 TYR E 36 PHE 0.013 0.002 PHE D 26 TRP 0.009 0.002 TRP H 84 HIS 0.007 0.002 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00665 (16214) covalent geometry : angle 0.53110 (21791) hydrogen bonds : bond 0.04874 ( 776) hydrogen bonds : angle 4.34293 ( 2250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 0.631 Fit side-chains REVERT: B 77 GLU cc_start: 0.8023 (mp0) cc_final: 0.7511 (mp0) REVERT: B 100 ASN cc_start: 0.8304 (t0) cc_final: 0.8069 (t0) REVERT: C 77 GLU cc_start: 0.8075 (mp0) cc_final: 0.7622 (mp0) REVERT: C 100 ASN cc_start: 0.8237 (t0) cc_final: 0.7941 (t0) REVERT: C 202 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7418 (tm-30) REVERT: D 81 TYR cc_start: 0.8773 (p90) cc_final: 0.8456 (p90) REVERT: D 190 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7917 (mtpp) REVERT: D 202 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7258 (tm-30) REVERT: E 76 ASN cc_start: 0.8577 (m-40) cc_final: 0.8340 (m-40) REVERT: F 100 ASN cc_start: 0.8463 (t0) cc_final: 0.8188 (t0) REVERT: G 77 GLU cc_start: 0.8081 (mp0) cc_final: 0.7822 (mp0) REVERT: G 100 ASN cc_start: 0.8416 (t0) cc_final: 0.8134 (t0) REVERT: G 133 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8549 (mtpp) REVERT: H 62 LYS cc_start: 0.8375 (tttt) cc_final: 0.8150 (tttt) REVERT: H 67 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7319 (mt-10) REVERT: H 133 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (mtpp) REVERT: H 202 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7065 (tm-30) REVERT: I 56 MET cc_start: 0.7327 (mmm) cc_final: 0.7100 (tmm) REVERT: I 204 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7078 (ttp80) REVERT: J 100 ASN cc_start: 0.8402 (t0) cc_final: 0.8127 (t0) REVERT: J 201 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: K 100 ASN cc_start: 0.8487 (t0) cc_final: 0.8184 (t0) REVERT: K 202 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7418 (tm-30) outliers start: 38 outliers final: 31 residues processed: 320 average time/residue: 0.7650 time to fit residues: 262.5112 Evaluate side-chains 340 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 70 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN K 37 GLN K 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.147696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128655 restraints weight = 19867.702| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.75 r_work: 0.3666 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16214 Z= 0.128 Angle : 0.466 9.818 21791 Z= 0.251 Chirality : 0.040 0.133 2299 Planarity : 0.003 0.073 2882 Dihedral : 3.745 17.731 2255 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.02 % Allowed : 14.80 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.19), residues: 2002 helix: 2.42 (0.18), residues: 770 sheet: 0.84 (0.24), residues: 495 loop : 0.76 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 204 TYR 0.011 0.001 TYR E 36 PHE 0.006 0.001 PHE D 26 TRP 0.006 0.001 TRP H 84 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00293 (16214) covalent geometry : angle 0.46555 (21791) hydrogen bonds : bond 0.03554 ( 776) hydrogen bonds : angle 4.09537 ( 2250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 0.511 Fit side-chains REVERT: B 77 GLU cc_start: 0.8003 (mp0) cc_final: 0.7645 (mp0) REVERT: B 100 ASN cc_start: 0.8284 (t0) cc_final: 0.8051 (t0) REVERT: C 77 GLU cc_start: 0.8053 (mp0) cc_final: 0.7635 (mp0) REVERT: C 202 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 81 TYR cc_start: 0.8730 (p90) cc_final: 0.8395 (p90) REVERT: D 190 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7856 (mtpp) REVERT: D 202 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7147 (tm-30) REVERT: D 206 ASN cc_start: 0.8145 (m-40) cc_final: 0.7709 (m-40) REVERT: E 76 ASN cc_start: 0.8513 (m-40) cc_final: 0.8280 (m-40) REVERT: F 100 ASN cc_start: 0.8433 (t0) cc_final: 0.8161 (t0) REVERT: G 77 GLU cc_start: 0.8045 (mp0) cc_final: 0.7808 (mp0) REVERT: G 100 ASN cc_start: 0.8373 (t0) cc_final: 0.8092 (t0) REVERT: G 133 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8361 (mtpp) REVERT: H 62 LYS cc_start: 0.8376 (tttt) cc_final: 0.8132 (tttt) REVERT: H 67 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7200 (mt-10) REVERT: H 202 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7075 (tm-30) REVERT: J 100 ASN cc_start: 0.8324 (t0) cc_final: 0.8053 (t0) REVERT: J 201 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: K 100 ASN cc_start: 0.8439 (t0) cc_final: 0.8132 (t0) outliers start: 34 outliers final: 31 residues processed: 299 average time/residue: 0.7426 time to fit residues: 239.3320 Evaluate side-chains 320 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 2 optimal weight: 0.1980 chunk 188 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.146659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127999 restraints weight = 20167.814| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.74 r_work: 0.3662 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16214 Z= 0.149 Angle : 0.474 9.763 21791 Z= 0.256 Chirality : 0.040 0.149 2299 Planarity : 0.003 0.038 2882 Dihedral : 3.711 17.264 2255 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.08 % Allowed : 14.91 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.19), residues: 2002 helix: 2.42 (0.18), residues: 770 sheet: 0.87 (0.24), residues: 495 loop : 0.81 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 193 TYR 0.011 0.001 TYR E 36 PHE 0.008 0.001 PHE D 26 TRP 0.007 0.001 TRP H 84 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00344 (16214) covalent geometry : angle 0.47387 (21791) hydrogen bonds : bond 0.03700 ( 776) hydrogen bonds : angle 4.09953 ( 2250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 296 time to evaluate : 0.644 Fit side-chains REVERT: B 77 GLU cc_start: 0.8019 (mp0) cc_final: 0.7660 (mp0) REVERT: B 100 ASN cc_start: 0.8288 (t0) cc_final: 0.8053 (t0) REVERT: C 77 GLU cc_start: 0.8060 (mp0) cc_final: 0.7649 (mp0) REVERT: C 100 ASN cc_start: 0.8191 (t0) cc_final: 0.7896 (t0) REVERT: C 194 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6518 (pt0) REVERT: C 202 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 81 TYR cc_start: 0.8740 (p90) cc_final: 0.8406 (p90) REVERT: D 190 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7868 (mtpp) REVERT: D 202 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7110 (tm-30) REVERT: D 206 ASN cc_start: 0.8155 (m-40) cc_final: 0.7700 (m-40) REVERT: E 76 ASN cc_start: 0.8526 (m-40) cc_final: 0.8292 (m-40) REVERT: F 100 ASN cc_start: 0.8456 (t0) cc_final: 0.8181 (t0) REVERT: F 204 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7260 (ttp80) REVERT: G 77 GLU cc_start: 0.8078 (mp0) cc_final: 0.7842 (mp0) REVERT: G 100 ASN cc_start: 0.8388 (t0) cc_final: 0.8105 (t0) REVERT: G 133 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8355 (mtpp) REVERT: H 62 LYS cc_start: 0.8371 (tttt) cc_final: 0.8138 (tttt) REVERT: H 67 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7224 (mt-10) REVERT: H 202 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7071 (tm-30) REVERT: J 100 ASN cc_start: 0.8345 (t0) cc_final: 0.8072 (t0) REVERT: J 201 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: K 100 ASN cc_start: 0.8465 (t0) cc_final: 0.8162 (t0) outliers start: 35 outliers final: 31 residues processed: 308 average time/residue: 0.7610 time to fit residues: 251.7398 Evaluate side-chains 328 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain J residue 28 GLN Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN H 206 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.147859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128885 restraints weight = 19682.735| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.74 r_work: 0.3669 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16214 Z= 0.122 Angle : 0.461 9.812 21791 Z= 0.248 Chirality : 0.040 0.142 2299 Planarity : 0.003 0.037 2882 Dihedral : 3.661 17.134 2255 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.14 % Allowed : 15.03 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.19), residues: 2002 helix: 2.49 (0.18), residues: 770 sheet: 0.91 (0.24), residues: 495 loop : 0.84 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 193 TYR 0.011 0.001 TYR E 171 PHE 0.007 0.001 PHE D 26 TRP 0.006 0.001 TRP H 84 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00281 (16214) covalent geometry : angle 0.46069 (21791) hydrogen bonds : bond 0.03440 ( 776) hydrogen bonds : angle 4.04352 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6211.65 seconds wall clock time: 106 minutes 9.57 seconds (6369.57 seconds total)