Starting phenix.real_space_refine on Sat Jun 14 03:26:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tkq_41357/06_2025/8tkq_41357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tkq_41357/06_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_41357/06_2025/8tkq_41357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tkq_41357/06_2025/8tkq_41357.map" model { file = "/net/cci-nas-00/data/ceres_data/8tkq_41357/06_2025/8tkq_41357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tkq_41357/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.07, per 1000 atoms: 0.69 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: 4.54 Conformation dependent library (CDL) restraints added in 2.3 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: 2.67 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: 5.35 Time building geometry restraints manager: 5.07 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.750 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.200 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.890 ------------------------------------------------------------------------------- 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 : 1.995 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: 1.9308 time to fit residues: 739.8206 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 : 1.831 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.130825 restraints weight = 19781.086| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.78 r_work: 0.3687 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 : 1.718 Fit side-chains REVERT: A 201 GLU cc_start: 0.7060 (mp0) cc_final: 0.6691 (mp0) REVERT: B 77 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: B 100 ASN cc_start: 0.8277 (t0) cc_final: 0.7963 (t0) REVERT: C 62 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7931 (ttmm) REVERT: C 197 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7333 (mt-10) REVERT: C 202 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7306 (tm-30) REVERT: D 81 TYR cc_start: 0.8761 (p90) cc_final: 0.8468 (p90) REVERT: D 190 LYS cc_start: 0.8011 (mtpp) cc_final: 0.7717 (mtpp) REVERT: D 202 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7215 (tm-30) REVERT: E 76 ASN cc_start: 0.8478 (m-40) cc_final: 0.8256 (m-40) REVERT: F 100 ASN cc_start: 0.8512 (t0) cc_final: 0.8194 (t0) REVERT: G 100 ASN cc_start: 0.8278 (t0) cc_final: 0.7973 (t0) REVERT: H 100 ASN cc_start: 0.8380 (t0) cc_final: 0.8041 (t0) REVERT: H 197 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7316 (mt-10) REVERT: H 202 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7014 (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: 0.7118 (ttp80) REVERT: J 100 ASN cc_start: 0.8293 (t0) cc_final: 0.8000 (t0) REVERT: J 202 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7473 (tp30) REVERT: J 206 ASN cc_start: 0.8317 (m110) cc_final: 0.7927 (m110) REVERT: K 202 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7461 (tm-30) outliers start: 25 outliers final: 11 residues processed: 332 average time/residue: 2.0797 time to fit residues: 746.1499 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 : 2.677 ------------------------------------------------------------------------------- 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: 0.9980 chunk 59 optimal weight: 0.5980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 J 176 ASN K 76 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.147519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128769 restraints weight = 19682.964| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.74 r_work: 0.3660 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 16214 Z= 0.252 Angle : 0.518 6.522 21791 Z= 0.284 Chirality : 0.043 0.162 2299 Planarity : 0.003 0.042 2882 Dihedral : 4.068 16.779 2255 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.96 % Allowed : 9.86 % 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: 0.79 (0.19), residues: 2002 helix: 1.55 (0.19), residues: 770 sheet: 0.18 (0.23), residues: 495 loop : -0.21 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 84 HIS 0.007 0.002 HIS C 86 PHE 0.014 0.002 PHE D 26 TYR 0.016 0.002 TYR E 36 ARG 0.006 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 776) hydrogen bonds : angle 4.52344 ( 2250) covalent geometry : bond 0.00576 (16214) covalent geometry : angle 0.51808 (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 361 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 328 time to evaluate : 1.717 Fit side-chains REVERT: A 201 GLU cc_start: 0.7339 (mp0) cc_final: 0.7041 (mp0) REVERT: B 100 ASN cc_start: 0.8295 (t0) cc_final: 0.8020 (t0) REVERT: C 34 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7441 (mm-30) REVERT: C 62 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7934 (ttmm) REVERT: C 202 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7331 (tm-30) REVERT: D 81 TYR cc_start: 0.8805 (p90) cc_final: 0.8503 (p90) REVERT: D 190 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7801 (mtpp) REVERT: D 202 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7249 (tm-30) REVERT: E 76 ASN cc_start: 0.8573 (m-40) cc_final: 0.8305 (m-40) REVERT: E 197 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7065 (mm-30) REVERT: E 201 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: F 100 ASN cc_start: 0.8518 (t0) cc_final: 0.8209 (t0) REVERT: G 100 ASN cc_start: 0.8321 (t0) cc_final: 0.8038 (t0) REVERT: H 67 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7374 (mt-10) REVERT: H 100 ASN cc_start: 0.8405 (t0) cc_final: 0.8062 (t0) REVERT: H 202 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6963 (tm-30) REVERT: H 206 ASN cc_start: 0.8171 (m-40) cc_final: 0.7769 (m-40) REVERT: I 204 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.7058 (ttp80) REVERT: J 100 ASN cc_start: 0.8306 (t0) cc_final: 0.8024 (t0) REVERT: J 169 LYS cc_start: 0.7772 (mttm) cc_final: 0.7569 (mttm) REVERT: J 201 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: J 202 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7520 (tm-30) REVERT: J 206 ASN cc_start: 0.8362 (m110) cc_final: 0.8038 (m110) REVERT: K 202 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7425 (tm-30) outliers start: 33 outliers final: 23 residues processed: 333 average time/residue: 1.7793 time to fit residues: 635.8704 Evaluate side-chains 353 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 50 GLU 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 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: 3.9990 chunk 192 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.148080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130061 restraints weight = 19977.773| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.71 r_work: 0.3686 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1670 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= 0.125 Angle : 0.450 5.709 21791 Z= 0.245 Chirality : 0.040 0.131 2299 Planarity : 0.003 0.033 2882 Dihedral : 3.845 17.191 2255 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.90 % Allowed : 11.94 % Favored : 86.16 % 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: 1.30 (0.19), residues: 2002 helix: 1.94 (0.19), residues: 770 sheet: 0.42 (0.24), residues: 495 loop : 0.14 (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 G 86 PHE 0.009 0.001 PHE D 26 TYR 0.012 0.001 TYR E 36 ARG 0.005 0.000 ARG I 143 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 776) hydrogen bonds : angle 4.22720 ( 2250) covalent geometry : bond 0.00283 (16214) covalent geometry : angle 0.45021 (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 331 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 299 time to evaluate : 1.830 Fit side-chains REVERT: B 77 GLU cc_start: 0.7966 (mp0) cc_final: 0.7407 (mp0) REVERT: B 100 ASN cc_start: 0.8243 (t0) cc_final: 0.7970 (t0) REVERT: B 206 ASN cc_start: 0.8119 (m-40) cc_final: 0.7913 (m110) REVERT: C 34 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: C 62 LYS cc_start: 0.8209 (ttmm) cc_final: 0.8008 (ttmm) REVERT: C 77 GLU cc_start: 0.8095 (mp0) cc_final: 0.7647 (mp0) REVERT: C 202 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7375 (tm-30) REVERT: D 81 TYR cc_start: 0.8783 (p90) cc_final: 0.8461 (p90) REVERT: D 190 LYS cc_start: 0.8085 (mtpp) cc_final: 0.7798 (mtpp) REVERT: D 202 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7232 (tm-30) REVERT: E 76 ASN cc_start: 0.8503 (m-40) cc_final: 0.8267 (m-40) REVERT: E 197 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6942 (mm-30) REVERT: E 201 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: F 100 ASN cc_start: 0.8489 (t0) cc_final: 0.8176 (t0) REVERT: G 77 GLU cc_start: 0.8008 (mp0) cc_final: 0.7706 (mp0) REVERT: G 100 ASN cc_start: 0.8317 (t0) cc_final: 0.8034 (t0) REVERT: H 67 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7249 (mt-10) REVERT: H 100 ASN cc_start: 0.8424 (t0) cc_final: 0.8070 (t0) REVERT: H 202 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6966 (tm-30) REVERT: H 206 ASN cc_start: 0.8117 (m-40) cc_final: 0.7658 (m-40) REVERT: I 56 MET cc_start: 0.7134 (mmm) cc_final: 0.6845 (tmm) REVERT: J 100 ASN cc_start: 0.8301 (t0) cc_final: 0.8030 (t0) REVERT: J 169 LYS cc_start: 0.7722 (mttm) cc_final: 0.7521 (mmtm) REVERT: J 201 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: J 202 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7421 (tm-30) REVERT: J 206 ASN cc_start: 0.8365 (m110) cc_final: 0.8032 (m110) REVERT: K 202 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7416 (tm-30) outliers start: 32 outliers final: 20 residues processed: 307 average time/residue: 1.8534 time to fit residues: 617.7120 Evaluate side-chains 320 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 297 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 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 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 I residue 206 ASN 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: 0.0870 chunk 197 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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 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 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 = 0.3993 r_free = 0.3993 target = 0.147199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.127793 restraints weight = 20177.780| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.78 r_work: 0.3650 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16214 Z= 0.195 Angle : 0.483 7.599 21791 Z= 0.263 Chirality : 0.041 0.147 2299 Planarity : 0.003 0.038 2882 Dihedral : 3.865 16.357 2255 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.14 % Allowed : 12.18 % Favored : 85.68 % 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: 1.48 (0.19), residues: 2002 helix: 2.02 (0.19), residues: 770 sheet: 0.52 (0.24), residues: 495 loop : 0.34 (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 0.012 0.001 PHE D 26 TYR 0.014 0.002 TYR E 36 ARG 0.008 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 776) hydrogen bonds : angle 4.28742 ( 2250) covalent geometry : bond 0.00446 (16214) covalent geometry : angle 0.48289 (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 344 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 1.737 Fit side-chains REVERT: B 77 GLU cc_start: 0.8012 (mp0) cc_final: 0.7456 (mp0) REVERT: B 100 ASN cc_start: 0.8325 (t0) cc_final: 0.8084 (t0) REVERT: C 34 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: C 46 ARG cc_start: 0.8269 (mtt90) cc_final: 0.7975 (mtt-85) REVERT: C 77 GLU cc_start: 0.8072 (mp0) cc_final: 0.7612 (mp0) REVERT: C 202 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7436 (tm-30) REVERT: D 81 TYR cc_start: 0.8769 (p90) cc_final: 0.8456 (p90) REVERT: D 190 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7867 (mtpp) REVERT: D 202 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7320 (tm-30) REVERT: E 76 ASN cc_start: 0.8553 (m-40) cc_final: 0.8327 (m-40) REVERT: E 194 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: E 197 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7016 (mm-30) REVERT: E 201 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: F 100 ASN cc_start: 0.8536 (t0) cc_final: 0.8227 (t0) REVERT: G 77 GLU cc_start: 0.8020 (mp0) cc_final: 0.7738 (mp0) REVERT: G 100 ASN cc_start: 0.8388 (t0) cc_final: 0.8099 (t0) REVERT: H 62 LYS cc_start: 0.8377 (tttt) cc_final: 0.8132 (tttt) REVERT: H 67 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7260 (mt-10) REVERT: H 100 ASN cc_start: 0.8427 (t0) cc_final: 0.8089 (t0) REVERT: H 202 GLU cc_start: 0.7587 (tm-30) cc_final: 0.6996 (tm-30) REVERT: H 206 ASN cc_start: 0.8170 (m-40) cc_final: 0.7759 (m-40) REVERT: I 56 MET cc_start: 0.7245 (mmm) cc_final: 0.6974 (tmm) REVERT: J 100 ASN cc_start: 0.8338 (t0) cc_final: 0.8062 (t0) REVERT: J 201 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: J 202 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7518 (tm-30) REVERT: J 206 ASN cc_start: 0.8390 (m110) cc_final: 0.8093 (m110) REVERT: K 100 ASN cc_start: 0.8459 (t0) cc_final: 0.8118 (t0) REVERT: K 202 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7510 (tm-30) outliers start: 36 outliers final: 23 residues processed: 323 average time/residue: 1.7654 time to fit residues: 612.6957 Evaluate side-chains 331 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 304 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 119 SER 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 132 LEU Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 151 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 100 ASN D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN K 37 GLN K 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.148433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.129297 restraints weight = 19905.412| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.76 r_work: 0.3671 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1916 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= 0.111 Angle : 0.441 6.510 21791 Z= 0.240 Chirality : 0.039 0.174 2299 Planarity : 0.003 0.044 2882 Dihedral : 3.724 16.724 2255 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.44 % Allowed : 12.72 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 2002 helix: 2.25 (0.18), residues: 770 sheet: 0.65 (0.24), residues: 495 loop : 0.55 (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 0.008 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 0.03345 ( 776) hydrogen bonds : angle 4.10590 ( 2250) covalent geometry : bond 0.00250 (16214) covalent geometry : angle 0.44087 (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 329 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 1.897 Fit side-chains REVERT: B 77 GLU cc_start: 0.7985 (mp0) cc_final: 0.7461 (mp0) REVERT: B 100 ASN cc_start: 0.8325 (t0) cc_final: 0.8083 (t0) REVERT: C 77 GLU cc_start: 0.8030 (mp0) cc_final: 0.7582 (mp0) REVERT: C 202 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7405 (tm-30) REVERT: D 78 MET cc_start: 0.8468 (tpt) cc_final: 0.8187 (tpt) REVERT: D 81 TYR cc_start: 0.8749 (p90) cc_final: 0.8428 (p90) REVERT: D 190 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7840 (mtpp) REVERT: D 202 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7148 (tm-30) REVERT: D 206 ASN cc_start: 0.8179 (m-40) cc_final: 0.7756 (m-40) REVERT: E 76 ASN cc_start: 0.8516 (m-40) cc_final: 0.8284 (m-40) REVERT: E 197 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6964 (mm-30) REVERT: E 201 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: F 100 ASN cc_start: 0.8534 (t0) cc_final: 0.8231 (t0) REVERT: G 77 GLU cc_start: 0.8008 (mp0) cc_final: 0.7724 (mp0) REVERT: G 100 ASN cc_start: 0.8394 (t0) cc_final: 0.8107 (t0) REVERT: H 62 LYS cc_start: 0.8360 (tttt) cc_final: 0.8121 (tttt) REVERT: H 67 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7186 (mt-10) REVERT: H 77 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: H 100 ASN cc_start: 0.8471 (t0) cc_final: 0.8134 (t0) REVERT: H 202 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7003 (tm-30) REVERT: H 206 ASN cc_start: 0.8125 (m-40) cc_final: 0.7689 (m-40) REVERT: I 56 MET cc_start: 0.7196 (mmm) cc_final: 0.6964 (tmm) REVERT: J 100 ASN cc_start: 0.8302 (t0) cc_final: 0.8029 (t0) REVERT: J 201 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: K 100 ASN cc_start: 0.8421 (t0) cc_final: 0.8083 (t0) REVERT: K 202 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7432 (tm-30) outliers start: 41 outliers final: 30 residues processed: 304 average time/residue: 1.8583 time to fit residues: 606.0136 Evaluate side-chains 319 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 167 LEU Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 206 ASN 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=2.50 ------------------------------------------------------------------------------- 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: 0.7980 chunk 169 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 166 optimal weight: 0.1980 chunk 192 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 176 ASN K 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.149447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131301 restraints weight = 20182.968| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.67 r_work: 0.3681 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16214 Z= 0.100 Angle : 0.434 5.704 21791 Z= 0.235 Chirality : 0.039 0.172 2299 Planarity : 0.003 0.048 2882 Dihedral : 3.637 15.816 2255 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.14 % Allowed : 13.73 % Favored : 84.14 % 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: 2.00 (0.19), residues: 2002 helix: 2.39 (0.18), residues: 770 sheet: 0.80 (0.24), residues: 495 loop : 0.69 (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 0.007 0.001 PHE D 26 TYR 0.011 0.001 TYR E 171 ARG 0.011 0.000 ARG F 193 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 776) hydrogen bonds : angle 4.02871 ( 2250) covalent geometry : bond 0.00225 (16214) covalent geometry : angle 0.43442 (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 329 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 1.667 Fit side-chains REVERT: B 77 GLU cc_start: 0.7962 (mp0) cc_final: 0.7478 (mp0) REVERT: B 100 ASN cc_start: 0.8312 (t0) cc_final: 0.8068 (t0) REVERT: C 77 GLU cc_start: 0.8026 (mp0) cc_final: 0.7614 (mp0) REVERT: C 202 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7365 (tm-30) REVERT: D 81 TYR cc_start: 0.8729 (p90) cc_final: 0.8421 (p90) REVERT: D 190 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7840 (mtpp) REVERT: D 202 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7174 (tm-30) REVERT: D 206 ASN cc_start: 0.8158 (m-40) cc_final: 0.7724 (m-40) REVERT: E 197 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6985 (mm-30) REVERT: E 201 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: G 77 GLU cc_start: 0.8012 (mp0) cc_final: 0.7754 (mp0) REVERT: G 100 ASN cc_start: 0.8349 (t0) cc_final: 0.8066 (t0) REVERT: H 67 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7146 (mt-10) REVERT: H 77 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: H 100 ASN cc_start: 0.8437 (t0) cc_final: 0.8108 (t0) REVERT: H 202 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7028 (tm-30) REVERT: H 206 ASN cc_start: 0.8116 (m-40) cc_final: 0.7668 (m-40) REVERT: I 56 MET cc_start: 0.7246 (mmm) cc_final: 0.7032 (tmm) REVERT: J 100 ASN cc_start: 0.8275 (t0) cc_final: 0.8004 (t0) REVERT: J 201 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: K 100 ASN cc_start: 0.8388 (t0) cc_final: 0.8051 (t0) outliers start: 36 outliers final: 28 residues processed: 305 average time/residue: 1.7361 time to fit residues: 570.0976 Evaluate side-chains 320 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 ASP 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 100 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 77 GLU 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 133 LYS 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1319 > 50: distance: 148 - 249: 17.674 distance: 151 - 246: 10.922 distance: 164 - 230: 21.869 distance: 167 - 227: 12.408 distance: 171 - 172: 8.615 distance: 172 - 173: 4.530 distance: 172 - 175: 10.109 distance: 173 - 174: 6.773 distance: 173 - 180: 4.492 distance: 175 - 176: 12.529 distance: 176 - 177: 7.391 distance: 177 - 178: 15.095 distance: 180 - 181: 12.303 distance: 181 - 182: 4.467 distance: 181 - 184: 10.512 distance: 182 - 183: 4.925 distance: 182 - 188: 5.798 distance: 184 - 185: 5.833 distance: 185 - 186: 15.016 distance: 185 - 187: 28.068 distance: 188 - 189: 10.317 distance: 189 - 190: 13.115 distance: 189 - 192: 3.457 distance: 190 - 191: 13.634 distance: 190 - 197: 19.079 distance: 192 - 193: 8.475 distance: 193 - 194: 6.984 distance: 194 - 195: 10.133 distance: 195 - 196: 8.567 distance: 197 - 198: 22.268 distance: 198 - 199: 7.368 distance: 198 - 201: 6.821 distance: 199 - 200: 20.127 distance: 199 - 205: 8.381 distance: 201 - 202: 16.785 distance: 202 - 203: 5.158 distance: 202 - 204: 8.544 distance: 205 - 206: 14.161 distance: 206 - 207: 22.687 distance: 207 - 208: 25.373 distance: 207 - 209: 36.563 distance: 209 - 210: 41.696 distance: 210 - 211: 21.391 distance: 210 - 213: 27.456 distance: 211 - 212: 12.794 distance: 211 - 215: 5.355 distance: 213 - 214: 13.883 distance: 215 - 216: 14.695 distance: 216 - 217: 29.801 distance: 216 - 219: 10.438 distance: 217 - 218: 26.571 distance: 217 - 227: 6.319 distance: 219 - 220: 6.881 distance: 220 - 221: 5.237 distance: 220 - 222: 28.952 distance: 221 - 223: 7.921 distance: 222 - 224: 16.887 distance: 223 - 225: 26.631 distance: 224 - 225: 15.170 distance: 225 - 226: 11.111 distance: 227 - 228: 4.211 distance: 228 - 229: 15.089 distance: 228 - 231: 3.891 distance: 229 - 230: 8.640 distance: 229 - 237: 18.979 distance: 231 - 232: 5.970 distance: 232 - 233: 9.239 distance: 232 - 234: 9.922 distance: 233 - 235: 4.568 distance: 234 - 236: 7.590 distance: 235 - 236: 13.399 distance: 237 - 238: 7.645 distance: 238 - 239: 6.254 distance: 238 - 241: 7.894 distance: 239 - 240: 25.823 distance: 239 - 246: 7.725 distance: 241 - 242: 8.451 distance: 242 - 243: 5.257 distance: 243 - 245: 4.029 distance: 246 - 247: 6.570 distance: 247 - 248: 5.237 distance: 247 - 250: 13.757 distance: 248 - 249: 14.421 distance: 248 - 254: 6.474 distance: 250 - 251: 15.608 distance: 251 - 252: 14.130 distance: 251 - 253: 14.108