Starting phenix.real_space_refine on Sat May 17 13:06:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkq_41357/05_2025/8tkq_41357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkq_41357/05_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_41357/05_2025/8tkq_41357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkq_41357/05_2025/8tkq_41357.map" model { file = "/net/cci-nas-00/data/ceres_data/8tkq_41357/05_2025/8tkq_41357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkq_41357/05_2025/8tkq_41357.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.79, per 1000 atoms: 0.55 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: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.75 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: 4.71 Time building geometry restraints manager: 4.25 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' 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: 1.840 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.530 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.260 ------------------------------------------------------------------------------- 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 : 6.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (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 TRP 0.011 0.002 TRP H 84 HIS 0.009 0.002 HIS A 86 PHE 0.016 0.002 PHE D 26 TYR 0.017 0.002 TYR J 171 ARG 0.008 0.000 ARG I 55 Details of bonding type rmsd hydrogen bonds : bond 0.13465 ( 776) hydrogen bonds : angle 6.01994 ( 2250) covalent geometry : bond 0.00679 (16214) covalent geometry : angle 0.66001 (21791) *********************** 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 : 1.862 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: 0.7368 (t0) REVERT: C 202 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6793 (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: 1.7141 time to fit residues: 658.0102 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 : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 0.2980 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 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 K 181 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130818 restraints weight = 19781.086| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.76 r_work: 0.3687 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16214 Z= 0.129 Angle : 0.487 5.729 21791 Z= 0.265 Chirality : 0.040 0.141 2299 Planarity : 0.003 0.038 2882 Dihedral : 4.056 17.677 2255 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.49 % Allowed : 8.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 2002 helix: 1.28 (0.19), residues: 770 sheet: -0.03 (0.23), residues: 495 loop : -0.52 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 84 HIS 0.005 0.001 HIS C 86 PHE 0.009 0.001 PHE D 26 TYR 0.013 0.001 TYR E 36 ARG 0.005 0.000 ARG I 70 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 776) hydrogen bonds : angle 4.60864 ( 2250) covalent geometry : bond 0.00288 (16214) covalent geometry : angle 0.48665 (21791) *********************** 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 352 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 1.804 Fit side-chains REVERT: A 201 GLU cc_start: 0.7065 (mp0) cc_final: 0.6695 (mp0) REVERT: B 77 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: B 100 ASN cc_start: 0.8278 (t0) cc_final: 0.7962 (t0) REVERT: C 62 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7936 (ttmm) REVERT: C 197 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 202 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7304 (tm-30) REVERT: D 81 TYR cc_start: 0.8763 (p90) cc_final: 0.8471 (p90) REVERT: D 190 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7715 (mtpp) REVERT: D 202 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7216 (tm-30) REVERT: E 76 ASN cc_start: 0.8479 (m-40) cc_final: 0.8256 (m-40) REVERT: F 100 ASN cc_start: 0.8512 (t0) cc_final: 0.8195 (t0) REVERT: G 100 ASN cc_start: 0.8281 (t0) cc_final: 0.7976 (t0) REVERT: H 100 ASN cc_start: 0.8381 (t0) cc_final: 0.8042 (t0) REVERT: H 197 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7317 (mt-10) REVERT: H 202 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7016 (tm-30) REVERT: H 206 ASN cc_start: 0.8120 (m-40) cc_final: 0.7726 (m-40) REVERT: I 204 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7119 (ttp80) REVERT: J 100 ASN cc_start: 0.8294 (t0) cc_final: 0.8001 (t0) REVERT: J 202 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7475 (tp30) REVERT: J 206 ASN cc_start: 0.8318 (m110) cc_final: 0.7929 (m110) REVERT: K 202 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7462 (tm-30) outliers start: 25 outliers final: 11 residues processed: 332 average time/residue: 1.6540 time to fit residues: 592.6969 Evaluate side-chains 331 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 319 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 77 GLU 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 182 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 140 optimal weight: 0.0770 chunk 59 optimal weight: 0.5980 overall best weight: 1.6542 ------------------------------------------------------------------------------- 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 B 121 HIS B 176 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 90 GLN G 176 ASN H 91 GLN H 121 HIS J 90 GLN J 92 ASN K 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.147901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.129110 restraints weight = 19658.466| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.76 r_work: 0.3665 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16214 Z= 0.229 Angle : 0.507 6.401 21791 Z= 0.278 Chirality : 0.043 0.158 2299 Planarity : 0.003 0.041 2882 Dihedral : 4.032 16.592 2255 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.02 % Allowed : 9.80 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 2002 helix: 1.58 (0.19), residues: 770 sheet: 0.20 (0.23), residues: 495 loop : -0.20 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 84 HIS 0.006 0.002 HIS C 86 PHE 0.014 0.001 PHE D 26 TYR 0.015 0.002 TYR E 36 ARG 0.006 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 776) hydrogen bonds : angle 4.48897 ( 2250) covalent geometry : bond 0.00522 (16214) covalent geometry : angle 0.50731 (21791) *********************** 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 362 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 328 time to evaluate : 1.707 Fit side-chains REVERT: A 201 GLU cc_start: 0.7337 (mp0) cc_final: 0.7042 (mp0) REVERT: B 100 ASN cc_start: 0.8279 (t0) cc_final: 0.8003 (t0) REVERT: C 34 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: C 62 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7942 (ttmm) REVERT: C 202 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7362 (tm-30) REVERT: D 81 TYR cc_start: 0.8803 (p90) cc_final: 0.8505 (p90) REVERT: D 190 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7795 (mtpp) REVERT: D 202 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7248 (tm-30) REVERT: E 76 ASN cc_start: 0.8555 (m-40) cc_final: 0.8317 (m-40) REVERT: E 197 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7046 (mm-30) REVERT: E 201 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: F 100 ASN cc_start: 0.8508 (t0) cc_final: 0.8209 (t0) REVERT: G 100 ASN cc_start: 0.8320 (t0) cc_final: 0.8036 (t0) REVERT: H 56 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6608 (mmp) REVERT: H 67 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7357 (mt-10) REVERT: H 100 ASN cc_start: 0.8407 (t0) cc_final: 0.8063 (t0) REVERT: H 202 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6960 (tm-30) REVERT: H 206 ASN cc_start: 0.8164 (m-40) cc_final: 0.7763 (m-40) REVERT: I 204 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7059 (ttp80) REVERT: J 100 ASN cc_start: 0.8320 (t0) cc_final: 0.8041 (t0) REVERT: J 169 LYS cc_start: 0.7762 (mttm) cc_final: 0.7557 (mttm) REVERT: J 201 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: J 202 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7525 (tm-30) REVERT: J 206 ASN cc_start: 0.8360 (m110) cc_final: 0.8037 (m110) REVERT: K 202 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7501 (tm-30) outliers start: 34 outliers final: 21 residues processed: 333 average time/residue: 1.6993 time to fit residues: 609.1365 Evaluate side-chains 351 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 326 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 119 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 50 GLU 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 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 56 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 167 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 132 LEU 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 50 GLU 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 177 optimal weight: 8.9990 chunk 192 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 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 = 0.4006 r_free = 0.4006 target = 0.148507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130368 restraints weight = 19968.467| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.72 r_work: 0.3691 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16214 Z= 0.117 Angle : 0.443 5.714 21791 Z= 0.241 Chirality : 0.039 0.131 2299 Planarity : 0.003 0.033 2882 Dihedral : 3.804 17.067 2255 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.78 % Allowed : 11.76 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2002 helix: 2.00 (0.19), residues: 770 sheet: 0.44 (0.24), residues: 495 loop : 0.18 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 84 HIS 0.004 0.001 HIS G 86 PHE 0.009 0.001 PHE D 26 TYR 0.012 0.001 TYR E 36 ARG 0.004 0.000 ARG I 143 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 776) hydrogen bonds : angle 4.18258 ( 2250) covalent geometry : bond 0.00264 (16214) covalent geometry : angle 0.44266 (21791) *********************** 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 313 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 283 time to evaluate : 1.709 Fit side-chains REVERT: B 77 GLU cc_start: 0.7963 (mp0) cc_final: 0.7398 (mp0) REVERT: B 100 ASN cc_start: 0.8246 (t0) cc_final: 0.7970 (t0) REVERT: C 77 GLU cc_start: 0.8092 (mp0) cc_final: 0.7649 (mp0) REVERT: C 202 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7367 (tm-30) REVERT: D 81 TYR cc_start: 0.8778 (p90) cc_final: 0.8462 (p90) REVERT: D 190 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7805 (mtpp) REVERT: D 202 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7078 (tm-30) REVERT: D 206 ASN cc_start: 0.8129 (m-40) cc_final: 0.7692 (m-40) REVERT: E 76 ASN cc_start: 0.8491 (m-40) cc_final: 0.8249 (m-40) REVERT: E 192 LYS cc_start: 0.7841 (tttp) cc_final: 0.7595 (tttp) REVERT: E 197 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6989 (mm-30) REVERT: E 201 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: F 100 ASN cc_start: 0.8484 (t0) cc_final: 0.8173 (t0) REVERT: G 100 ASN cc_start: 0.8320 (t0) cc_final: 0.8032 (t0) REVERT: H 67 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7232 (mt-10) REVERT: H 100 ASN cc_start: 0.8414 (t0) cc_final: 0.8060 (t0) REVERT: H 202 GLU cc_start: 0.7562 (tm-30) cc_final: 0.6981 (tm-30) REVERT: H 206 ASN cc_start: 0.8109 (m-40) cc_final: 0.7673 (m-40) REVERT: I 56 MET cc_start: 0.7152 (mmm) cc_final: 0.6871 (tmm) REVERT: J 100 ASN cc_start: 0.8297 (t0) cc_final: 0.8023 (t0) REVERT: J 201 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: K 202 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7415 (tm-30) outliers start: 30 outliers final: 17 residues processed: 289 average time/residue: 1.7647 time to fit residues: 551.6609 Evaluate side-chains 300 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 281 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 56 MET 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 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 132 LEU 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 124 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 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 J 176 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 = 0.3989 r_free = 0.3989 target = 0.146730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127422 restraints weight = 20210.231| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.78 r_work: 0.3646 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16214 Z= 0.210 Angle : 0.482 5.968 21791 Z= 0.264 Chirality : 0.042 0.146 2299 Planarity : 0.003 0.042 2882 Dihedral : 3.879 16.318 2255 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.14 % Allowed : 12.06 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2002 helix: 2.03 (0.19), residues: 770 sheet: 0.51 (0.24), residues: 495 loop : 0.35 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 84 HIS 0.006 0.002 HIS C 86 PHE 0.011 0.001 PHE D 26 TYR 0.014 0.002 TYR E 36 ARG 0.007 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 776) hydrogen bonds : angle 4.30504 ( 2250) covalent geometry : bond 0.00480 (16214) covalent geometry : angle 0.48206 (21791) *********************** 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 347 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 1.824 Fit side-chains REVERT: B 77 GLU cc_start: 0.7987 (mp0) cc_final: 0.7480 (mp0) REVERT: B 100 ASN cc_start: 0.8326 (t0) cc_final: 0.8086 (t0) REVERT: C 46 ARG cc_start: 0.8304 (mtt90) cc_final: 0.8019 (mtt-85) REVERT: C 77 GLU cc_start: 0.8089 (mp0) cc_final: 0.7628 (mp0) REVERT: C 202 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7422 (tm-30) REVERT: D 81 TYR cc_start: 0.8767 (p90) cc_final: 0.8454 (p90) REVERT: D 190 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7871 (mtpp) REVERT: D 202 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7303 (tm-30) REVERT: E 76 ASN cc_start: 0.8557 (m-40) cc_final: 0.8327 (m-40) REVERT: E 194 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: E 197 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7057 (mm-30) REVERT: F 100 ASN cc_start: 0.8553 (t0) cc_final: 0.8243 (t0) REVERT: G 77 GLU cc_start: 0.8014 (mp0) cc_final: 0.7733 (mp0) REVERT: G 100 ASN cc_start: 0.8383 (t0) cc_final: 0.8095 (t0) REVERT: H 67 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7269 (mt-10) REVERT: H 100 ASN cc_start: 0.8466 (t0) cc_final: 0.8130 (t0) REVERT: H 202 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7006 (tm-30) REVERT: H 206 ASN cc_start: 0.8169 (m-40) cc_final: 0.7771 (m-40) REVERT: I 56 MET cc_start: 0.7247 (mmm) cc_final: 0.6975 (tmm) REVERT: J 100 ASN cc_start: 0.8369 (t0) cc_final: 0.8086 (t0) REVERT: J 201 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: J 202 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7537 (tp30) REVERT: J 206 ASN cc_start: 0.8255 (m-40) cc_final: 0.8016 (m-40) REVERT: K 100 ASN cc_start: 0.8478 (t0) cc_final: 0.8141 (t0) REVERT: K 202 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7484 (tm-30) outliers start: 36 outliers final: 25 residues processed: 325 average time/residue: 1.6724 time to fit residues: 584.2094 Evaluate side-chains 334 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 307 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 119 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 E residue 194 GLN 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 167 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 201 GLU 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 132 LEU 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 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 50 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 151 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 86 HIS D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN H 91 GLN 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 = 0.4019 r_free = 0.4019 target = 0.148778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130606 restraints weight = 20121.163| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.68 r_work: 0.3695 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2083 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= 0.082 Angle : 0.423 6.804 21791 Z= 0.229 Chirality : 0.039 0.196 2299 Planarity : 0.003 0.041 2882 Dihedral : 3.634 16.585 2255 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.90 % Allowed : 13.43 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 2002 helix: 2.38 (0.18), residues: 770 sheet: 0.73 (0.24), residues: 495 loop : 0.58 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 84 HIS 0.004 0.001 HIS G 86 PHE 0.007 0.001 PHE D 26 TYR 0.011 0.001 TYR E 171 ARG 0.009 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 776) hydrogen bonds : angle 3.99890 ( 2250) covalent geometry : bond 0.00181 (16214) covalent geometry : angle 0.42319 (21791) *********************** 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 331 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 299 time to evaluate : 1.725 Fit side-chains REVERT: B 77 GLU cc_start: 0.7947 (mp0) cc_final: 0.7461 (mp0) REVERT: B 100 ASN cc_start: 0.8253 (t0) cc_final: 0.8014 (t0) REVERT: C 77 GLU cc_start: 0.8018 (mp0) cc_final: 0.7614 (mp0) REVERT: C 202 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7328 (tm-30) REVERT: D 78 MET cc_start: 0.8413 (tpt) cc_final: 0.8145 (tpt) REVERT: D 81 TYR cc_start: 0.8715 (p90) cc_final: 0.8442 (p90) REVERT: D 190 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7808 (mtpp) REVERT: D 202 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 206 ASN cc_start: 0.8145 (m-40) cc_final: 0.7707 (m-40) REVERT: F 100 ASN cc_start: 0.8509 (t0) cc_final: 0.8204 (t0) REVERT: G 77 GLU cc_start: 0.7964 (mp0) cc_final: 0.7685 (mp0) REVERT: G 100 ASN cc_start: 0.8361 (t0) cc_final: 0.8065 (t0) REVERT: H 67 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7072 (mt-10) REVERT: H 100 ASN cc_start: 0.8430 (t0) cc_final: 0.8093 (t0) REVERT: H 202 GLU cc_start: 0.7539 (tm-30) cc_final: 0.6983 (tm-30) REVERT: H 206 ASN cc_start: 0.8086 (m-40) cc_final: 0.7650 (m-40) REVERT: I 56 MET cc_start: 0.7177 (mmm) cc_final: 0.6947 (tmm) REVERT: I 63 VAL cc_start: 0.8443 (t) cc_final: 0.8062 (m) REVERT: J 100 ASN cc_start: 0.8255 (t0) cc_final: 0.7975 (t0) REVERT: J 201 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: K 100 ASN cc_start: 0.8361 (t0) cc_final: 0.8015 (t0) outliers start: 32 outliers final: 21 residues processed: 312 average time/residue: 1.6526 time to fit residues: 555.6305 Evaluate side-chains 313 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 291 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 D residue 132 LEU Chi-restraints excluded: chain E residue 132 LEU 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 132 LEU Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 201 GLU 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 175 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 B 206 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 = 0.3988 r_free = 0.3988 target = 0.146693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127424 restraints weight = 19860.377| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.74 r_work: 0.3648 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16214 Z= 0.215 Angle : 0.493 6.149 21791 Z= 0.269 Chirality : 0.042 0.154 2299 Planarity : 0.003 0.049 2882 Dihedral : 3.814 16.351 2255 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.32 % Allowed : 14.08 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 2002 helix: 2.22 (0.18), residues: 770 sheet: 0.75 (0.24), residues: 495 loop : 0.63 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 84 HIS 0.006 0.002 HIS C 86 PHE 0.011 0.001 PHE I 26 TYR 0.015 0.002 TYR H 36 ARG 0.011 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 776) hydrogen bonds : angle 4.24787 ( 2250) covalent geometry : bond 0.00496 (16214) covalent geometry : angle 0.49289 (21791) *********************** 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 342 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 1.882 Fit side-chains REVERT: B 77 GLU cc_start: 0.8010 (mp0) cc_final: 0.7526 (mp0) REVERT: B 100 ASN cc_start: 0.8305 (t0) cc_final: 0.8066 (t0) REVERT: C 77 GLU cc_start: 0.8060 (mp0) cc_final: 0.7595 (mp0) REVERT: C 102 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7938 (mmtp) REVERT: C 202 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 81 TYR cc_start: 0.8749 (p90) cc_final: 0.8435 (p90) REVERT: D 190 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7879 (mtpp) REVERT: D 202 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7288 (tm-30) REVERT: E 76 ASN cc_start: 0.8575 (m-40) cc_final: 0.8358 (m-40) REVERT: F 100 ASN cc_start: 0.8553 (t0) cc_final: 0.8252 (t0) REVERT: G 100 ASN cc_start: 0.8383 (t0) cc_final: 0.8101 (t0) REVERT: H 62 LYS cc_start: 0.8382 (tttt) cc_final: 0.8146 (tttt) REVERT: H 67 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7269 (mt-10) REVERT: H 100 ASN cc_start: 0.8461 (t0) cc_final: 0.8146 (t0) REVERT: H 202 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6990 (tm-30) REVERT: H 206 ASN cc_start: 0.8181 (m-40) cc_final: 0.7776 (m-40) REVERT: I 56 MET cc_start: 0.7302 (mmm) cc_final: 0.7071 (tmm) REVERT: J 100 ASN cc_start: 0.8360 (t0) cc_final: 0.8087 (t0) REVERT: J 201 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: K 100 ASN cc_start: 0.8464 (t0) cc_final: 0.8145 (t0) REVERT: K 202 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7393 (tm-30) outliers start: 39 outliers final: 25 residues processed: 318 average time/residue: 1.6843 time to fit residues: 576.6780 Evaluate side-chains 328 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 C residue 56 MET Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain F residue 56 MET 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 132 LEU 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 201 GLU Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 56 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 176 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 133 optimal weight: 0.1980 chunk 18 optimal weight: 0.0870 chunk 117 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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** E 90 GLN E 92 ASN G 76 ASN G 176 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 = 0.148739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129646 restraints weight = 19756.667| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.76 r_work: 0.3676 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2170 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= 0.096 Angle : 0.445 8.885 21791 Z= 0.239 Chirality : 0.039 0.147 2299 Planarity : 0.003 0.055 2882 Dihedral : 3.653 16.504 2255 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.90 % Allowed : 15.15 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 2002 helix: 2.45 (0.18), residues: 770 sheet: 0.85 (0.24), residues: 495 loop : 0.77 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 84 HIS 0.004 0.001 HIS G 86 PHE 0.006 0.001 PHE D 26 TYR 0.011 0.001 TYR E 171 ARG 0.010 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 776) hydrogen bonds : angle 4.03313 ( 2250) covalent geometry : bond 0.00220 (16214) covalent geometry : angle 0.44549 (21791) *********************** 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 336 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 304 time to evaluate : 1.718 Fit side-chains REVERT: B 77 GLU cc_start: 0.7979 (mp0) cc_final: 0.7660 (mp0) REVERT: B 100 ASN cc_start: 0.8325 (t0) cc_final: 0.8080 (t0) REVERT: C 77 GLU cc_start: 0.8058 (mp0) cc_final: 0.7627 (mp0) REVERT: C 100 ASN cc_start: 0.8152 (t0) cc_final: 0.7847 (t0) REVERT: C 202 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7360 (tm-30) REVERT: D 81 TYR cc_start: 0.8720 (p90) cc_final: 0.8420 (p90) REVERT: D 190 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7856 (mtpp) REVERT: D 202 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 206 ASN cc_start: 0.8158 (m-40) cc_final: 0.7696 (m-40) REVERT: E 76 ASN cc_start: 0.8529 (m-40) cc_final: 0.8304 (m-40) REVERT: E 192 LYS cc_start: 0.7629 (tttp) cc_final: 0.7409 (tttp) REVERT: F 100 ASN cc_start: 0.8559 (t0) cc_final: 0.8255 (t0) REVERT: G 100 ASN cc_start: 0.8386 (t0) cc_final: 0.8105 (t0) REVERT: G 133 LYS cc_start: 0.8501 (mtpp) cc_final: 0.8294 (mtpp) REVERT: H 67 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7153 (mt-10) REVERT: H 100 ASN cc_start: 0.8453 (t0) cc_final: 0.8117 (t0) REVERT: H 202 GLU cc_start: 0.7544 (tm-30) cc_final: 0.6978 (tm-30) REVERT: H 206 ASN cc_start: 0.8111 (m-40) cc_final: 0.7687 (m-40) REVERT: I 56 MET cc_start: 0.7273 (mmm) cc_final: 0.7064 (tmm) REVERT: I 62 LYS cc_start: 0.8180 (tttm) cc_final: 0.7955 (tttm) REVERT: J 100 ASN cc_start: 0.8308 (t0) cc_final: 0.8033 (t0) REVERT: J 201 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: K 100 ASN cc_start: 0.8425 (t0) cc_final: 0.8106 (t0) REVERT: K 202 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7384 (tm-30) outliers start: 32 outliers final: 25 residues processed: 314 average time/residue: 1.7583 time to fit residues: 594.4124 Evaluate side-chains 327 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 301 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D 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 124 VAL Chi-restraints excluded: chain I residue 132 LEU 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 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 180 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** F 176 ASN 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 = 0.3993 r_free = 0.3993 target = 0.146978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.128314 restraints weight = 20044.777| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.72 r_work: 0.3665 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16214 Z= 0.147 Angle : 0.474 8.865 21791 Z= 0.255 Chirality : 0.040 0.157 2299 Planarity : 0.003 0.053 2882 Dihedral : 3.684 16.416 2255 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.66 % Allowed : 15.92 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 2002 helix: 2.41 (0.18), residues: 770 sheet: 0.89 (0.24), residues: 495 loop : 0.80 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 84 HIS 0.004 0.001 HIS C 86 PHE 0.009 0.001 PHE I 26 TYR 0.011 0.001 TYR E 171 ARG 0.014 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 776) hydrogen bonds : angle 4.09226 ( 2250) covalent geometry : bond 0.00340 (16214) covalent geometry : angle 0.47363 (21791) *********************** 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 340 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 312 time to evaluate : 1.840 Fit side-chains REVERT: B 77 GLU cc_start: 0.7996 (mp0) cc_final: 0.7677 (mp0) REVERT: B 100 ASN cc_start: 0.8345 (t0) cc_final: 0.8108 (t0) REVERT: C 77 GLU cc_start: 0.8034 (mp0) cc_final: 0.7604 (mp0) REVERT: C 100 ASN cc_start: 0.8155 (t0) cc_final: 0.7854 (t0) REVERT: C 202 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7368 (tm-30) REVERT: D 81 TYR cc_start: 0.8739 (p90) cc_final: 0.8438 (p90) REVERT: D 190 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7857 (mtpp) REVERT: D 202 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7090 (tm-30) REVERT: D 206 ASN cc_start: 0.8148 (m-40) cc_final: 0.7674 (m-40) REVERT: E 76 ASN cc_start: 0.8545 (m-40) cc_final: 0.8342 (m-40) REVERT: F 100 ASN cc_start: 0.8554 (t0) cc_final: 0.8258 (t0) REVERT: G 100 ASN cc_start: 0.8386 (t0) cc_final: 0.8107 (t0) REVERT: G 133 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8357 (mtpp) REVERT: H 62 LYS cc_start: 0.8363 (tttt) cc_final: 0.8136 (tttt) REVERT: H 67 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7210 (mt-10) REVERT: H 100 ASN cc_start: 0.8458 (t0) cc_final: 0.8141 (t0) REVERT: H 202 GLU cc_start: 0.7552 (tm-30) cc_final: 0.6985 (tm-30) REVERT: H 206 ASN cc_start: 0.8145 (m-40) cc_final: 0.7746 (m-40) REVERT: I 56 MET cc_start: 0.7288 (mmm) cc_final: 0.7083 (tmm) REVERT: J 100 ASN cc_start: 0.8319 (t0) cc_final: 0.8046 (t0) REVERT: J 201 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: K 100 ASN cc_start: 0.8447 (t0) cc_final: 0.8136 (t0) outliers start: 28 outliers final: 23 residues processed: 320 average time/residue: 1.7491 time to fit residues: 600.9336 Evaluate side-chains 336 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 312 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D 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 32 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 132 LEU 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 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 14 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 165 optimal weight: 0.0770 chunk 133 optimal weight: 0.5980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 91 GLN ** 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 = 0.4009 r_free = 0.4009 target = 0.148064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129445 restraints weight = 20153.732| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.71 r_work: 0.3686 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16214 Z= 0.089 Angle : 0.450 8.713 21791 Z= 0.240 Chirality : 0.039 0.143 2299 Planarity : 0.003 0.045 2882 Dihedral : 3.579 16.653 2255 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.54 % Allowed : 16.22 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 2002 helix: 2.56 (0.18), residues: 770 sheet: 0.97 (0.25), residues: 495 loop : 0.89 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 84 HIS 0.004 0.001 HIS G 86 PHE 0.006 0.001 PHE D 26 TYR 0.011 0.001 TYR E 171 ARG 0.013 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 776) hydrogen bonds : angle 3.95648 ( 2250) covalent geometry : bond 0.00205 (16214) covalent geometry : angle 0.45050 (21791) ********************** 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 326 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 300 time to evaluate : 1.752 Fit side-chains REVERT: A 206 ASN cc_start: 0.7950 (m-40) cc_final: 0.7613 (m-40) REVERT: B 77 GLU cc_start: 0.7967 (mp0) cc_final: 0.7528 (mp0) REVERT: B 100 ASN cc_start: 0.8297 (t0) cc_final: 0.8058 (t0) REVERT: C 77 GLU cc_start: 0.8019 (mp0) cc_final: 0.7589 (mp0) REVERT: C 202 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 81 TYR cc_start: 0.8710 (p90) cc_final: 0.8462 (p90) REVERT: D 190 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7857 (mtpp) REVERT: D 202 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7105 (tm-30) REVERT: D 206 ASN cc_start: 0.8130 (m-40) cc_final: 0.7688 (m-40) REVERT: E 76 ASN cc_start: 0.8515 (m-40) cc_final: 0.8309 (m-40) REVERT: E 192 LYS cc_start: 0.7709 (tttp) cc_final: 0.7453 (tttp) REVERT: G 100 ASN cc_start: 0.8389 (t0) cc_final: 0.8105 (t0) REVERT: G 133 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8124 (mtpp) REVERT: H 62 LYS cc_start: 0.8399 (tttt) cc_final: 0.8175 (tttt) REVERT: H 67 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7136 (mt-10) REVERT: H 100 ASN cc_start: 0.8443 (t0) cc_final: 0.8110 (t0) REVERT: H 202 GLU cc_start: 0.7529 (tm-30) cc_final: 0.6989 (tm-30) REVERT: H 206 ASN cc_start: 0.8100 (m-40) cc_final: 0.7670 (m-40) REVERT: I 56 MET cc_start: 0.7258 (mmm) cc_final: 0.7049 (tmm) REVERT: J 100 ASN cc_start: 0.8285 (t0) cc_final: 0.8002 (t0) REVERT: J 201 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: K 100 ASN cc_start: 0.8423 (t0) cc_final: 0.8110 (t0) outliers start: 26 outliers final: 23 residues processed: 309 average time/residue: 1.7156 time to fit residues: 569.9933 Evaluate side-chains 321 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 297 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain F residue 56 MET 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 32 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 132 LEU 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 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 69 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 160 optimal weight: 0.0770 chunk 130 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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** F 176 ASN G 76 ASN G 176 ASN H 45 GLN H 91 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 = 0.3986 r_free = 0.3986 target = 0.145882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127677 restraints weight = 20165.111| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.67 r_work: 0.3659 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16214 Z= 0.197 Angle : 0.501 8.492 21791 Z= 0.270 Chirality : 0.042 0.152 2299 Planarity : 0.003 0.045 2882 Dihedral : 3.744 17.875 2255 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.78 % Allowed : 16.22 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.19), residues: 2002 helix: 2.40 (0.18), residues: 770 sheet: 0.94 (0.24), residues: 495 loop : 0.88 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 84 HIS 0.006 0.002 HIS C 86 PHE 0.010 0.001 PHE I 26 TYR 0.012 0.002 TYR H 36 ARG 0.014 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 776) hydrogen bonds : angle 4.16762 ( 2250) covalent geometry : bond 0.00456 (16214) covalent geometry : angle 0.50066 (21791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14343.07 seconds wall clock time: 246 minutes 44.58 seconds (14804.58 seconds total)