Starting phenix.real_space_refine on Mon Nov 18 06:52:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkq_41357/11_2024/8tkq_41357.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkq_41357/11_2024/8tkq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkq_41357/11_2024/8tkq_41357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkq_41357/11_2024/8tkq_41357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkq_41357/11_2024/8tkq_41357.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkq_41357/11_2024/8tkq_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-5513/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: 9.35, per 1000 atoms: 0.59 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: 3.62 Conformation dependent library (CDL) restraints added in 2.1 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: 1.52 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: 4.48 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5445 1.34 - 1.46: 2750 1.46 - 1.57: 7909 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 16214 Sorted by residual: bond pdb=" CA GLY I 83 " pdb=" C GLY I 83 " ideal model delta sigma weight residual 1.514 1.496 0.018 1.41e-02 5.03e+03 1.62e+00 bond pdb=" CA GLY J 125 " pdb=" C GLY J 125 " ideal model delta sigma weight residual 1.516 1.506 0.010 8.20e-03 1.49e+04 1.59e+00 bond pdb=" CA GLY K 83 " pdb=" C GLY K 83 " ideal model delta sigma weight residual 1.514 1.497 0.017 1.41e-02 5.03e+03 1.44e+00 bond pdb=" N GLN K 28 " pdb=" CA GLN K 28 " ideal model delta sigma weight residual 1.458 1.446 0.012 1.08e-02 8.57e+03 1.25e+00 bond pdb=" CG GLN E 91 " pdb=" CD GLN E 91 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.14e+00 ... (remaining 16209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 21143 1.64 - 3.27: 584 3.27 - 4.91: 43 4.91 - 6.54: 13 6.54 - 8.18: 8 Bond angle restraints: 21791 Sorted by residual: angle pdb=" C GLY I 131 " pdb=" N LEU I 132 " pdb=" CA LEU I 132 " ideal model delta sigma weight residual 121.31 129.49 -8.18 1.49e+00 4.50e-01 3.01e+01 angle pdb=" C GLY H 131 " pdb=" N LEU H 132 " pdb=" CA LEU H 132 " ideal model delta sigma weight residual 121.31 129.35 -8.04 1.49e+00 4.50e-01 2.91e+01 angle pdb=" C GLY E 131 " pdb=" N LEU E 132 " pdb=" CA LEU E 132 " ideal model delta sigma weight residual 121.31 128.67 -7.36 1.49e+00 4.50e-01 2.44e+01 angle pdb=" N LEU E 132 " pdb=" CA LEU E 132 " pdb=" C LEU E 132 " ideal model delta sigma weight residual 110.35 116.36 -6.01 1.40e+00 5.10e-01 1.84e+01 angle pdb=" N LEU I 132 " pdb=" CA LEU I 132 " pdb=" C LEU I 132 " ideal model delta sigma weight residual 110.35 116.10 -5.75 1.40e+00 5.10e-01 1.69e+01 ... (remaining 21786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 8787 16.30 - 32.61: 817 32.61 - 48.91: 136 48.91 - 65.21: 37 65.21 - 81.52: 24 Dihedral angle restraints: 9801 sinusoidal: 4004 harmonic: 5797 Sorted by residual: dihedral pdb=" CA GLY I 131 " pdb=" C GLY I 131 " pdb=" N LEU I 132 " pdb=" CA LEU I 132 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLY F 131 " pdb=" C GLY F 131 " pdb=" N LEU F 132 " pdb=" CA LEU F 132 " ideal model delta harmonic sigma weight residual 180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLY D 131 " pdb=" C GLY D 131 " pdb=" N LEU D 132 " pdb=" CA LEU D 132 " ideal model delta harmonic sigma weight residual -180.00 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 9798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1191 0.030 - 0.061: 752 0.061 - 0.091: 243 0.091 - 0.122: 93 0.122 - 0.152: 20 Chirality restraints: 2299 Sorted by residual: chirality pdb=" CA PRO F 198 " pdb=" N PRO F 198 " pdb=" C PRO F 198 " pdb=" CB PRO F 198 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA PRO I 198 " pdb=" N PRO I 198 " pdb=" C PRO I 198 " pdb=" CB PRO I 198 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA PRO A 198 " pdb=" N PRO A 198 " pdb=" C PRO A 198 " pdb=" CB PRO A 198 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 2296 not shown) Planarity restraints: 2882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 197 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO G 198 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO G 198 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 198 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 86 " 0.015 2.00e-02 2.50e+03 1.22e-02 2.23e+00 pdb=" CG HIS C 86 " -0.024 2.00e-02 2.50e+03 pdb=" ND1 HIS C 86 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS C 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 86 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS C 86 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 86 " 0.012 2.00e-02 2.50e+03 1.08e-02 1.76e+00 pdb=" CG HIS A 86 " -0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 86 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 86 " 0.003 2.00e-02 2.50e+03 ... (remaining 2879 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 512 2.71 - 3.26: 15163 3.26 - 3.81: 25617 3.81 - 4.35: 33257 4.35 - 4.90: 56606 Nonbonded interactions: 131155 Sorted by model distance: nonbonded pdb=" O LEU F 47 " pdb=" OH TYR F 171 " model vdw 2.166 3.040 nonbonded pdb=" O LEU H 47 " pdb=" OH TYR H 171 " model vdw 2.179 3.040 nonbonded pdb=" O LEU E 47 " pdb=" OH TYR E 171 " model vdw 2.189 3.040 nonbonded pdb=" O LEU J 47 " pdb=" OH TYR J 171 " model vdw 2.208 3.040 nonbonded pdb=" O LEU A 47 " pdb=" OH TYR A 171 " model vdw 2.226 3.040 ... (remaining 131150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.020 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.110 ------------------------------------------------------------------------------- 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= 0.440 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 *********************** 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 : 1.708 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: 1.8736 time to fit residues: 718.3659 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 : 1.736 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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= 0.186 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 *********************** 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 : 1.756 Fit side-chains REVERT: A 201 GLU cc_start: 0.6388 (mp0) cc_final: 0.6033 (mp0) REVERT: B 77 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: B 100 ASN cc_start: 0.7643 (t0) cc_final: 0.7303 (t0) REVERT: C 62 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7783 (ttmm) REVERT: C 202 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6885 (tm-30) REVERT: D 81 TYR cc_start: 0.8677 (p90) cc_final: 0.8320 (p90) REVERT: D 190 LYS cc_start: 0.7613 (mtpp) cc_final: 0.7392 (mtpp) REVERT: D 202 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6976 (tm-30) REVERT: E 76 ASN cc_start: 0.8374 (m-40) cc_final: 0.8137 (m-40) REVERT: F 100 ASN cc_start: 0.7697 (t0) cc_final: 0.7395 (t0) REVERT: G 100 ASN cc_start: 0.7588 (t0) cc_final: 0.7279 (t0) REVERT: H 100 ASN cc_start: 0.7739 (t0) cc_final: 0.7392 (t0) REVERT: H 202 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6568 (tm-30) REVERT: H 206 ASN cc_start: 0.7872 (m-40) cc_final: 0.7364 (m-40) REVERT: I 204 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.6969 (ttp80) REVERT: J 100 ASN cc_start: 0.7614 (t0) cc_final: 0.7319 (t0) REVERT: J 202 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7158 (tp30) REVERT: J 206 ASN cc_start: 0.8021 (m110) cc_final: 0.7601 (m110) REVERT: K 202 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7147 (tm-30) outliers start: 25 outliers final: 11 residues processed: 332 average time/residue: 1.7579 time to fit residues: 628.6141 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 : 1.871 ------------------------------------------------------------------------------- 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 99 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 144 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1384 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= 0.377 Angle : 0.519 6.546 21791 Z= 0.284 Chirality : 0.043 0.162 2299 Planarity : 0.003 0.043 2882 Dihedral : 4.077 16.832 2255 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.02 % Allowed : 9.86 % Favored : 88.12 % 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 0.008 0.002 HIS C 86 PHE 0.015 0.002 PHE D 26 TYR 0.015 0.002 TYR E 36 ARG 0.006 0.000 ARG C 193 *********************** 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 363 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 329 time to evaluate : 1.675 Fit side-chains REVERT: A 201 GLU cc_start: 0.6647 (mp0) cc_final: 0.6366 (mp0) REVERT: B 100 ASN cc_start: 0.7692 (t0) cc_final: 0.7404 (t0) REVERT: C 34 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6874 (mm-30) REVERT: C 62 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7804 (ttmm) REVERT: C 202 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6935 (tm-30) REVERT: D 81 TYR cc_start: 0.8720 (p90) cc_final: 0.8370 (p90) REVERT: D 190 LYS cc_start: 0.7715 (mtpp) cc_final: 0.7491 (mtpp) REVERT: D 202 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6977 (tm-30) REVERT: E 76 ASN cc_start: 0.8478 (m-40) cc_final: 0.8198 (m-40) REVERT: E 197 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6740 (mm-30) REVERT: E 201 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: F 100 ASN cc_start: 0.7746 (t0) cc_final: 0.7451 (t0) REVERT: G 100 ASN cc_start: 0.7646 (t0) cc_final: 0.7356 (t0) REVERT: H 100 ASN cc_start: 0.7792 (t0) cc_final: 0.7444 (t0) REVERT: H 202 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6529 (tm-30) REVERT: H 206 ASN cc_start: 0.7942 (m-40) cc_final: 0.7423 (m-40) REVERT: J 100 ASN cc_start: 0.7628 (t0) cc_final: 0.7340 (t0) REVERT: J 201 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: J 202 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7211 (tm-30) REVERT: J 206 ASN cc_start: 0.8105 (m110) cc_final: 0.7752 (m110) REVERT: K 202 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7199 (tm-30) outliers start: 34 outliers final: 24 residues processed: 335 average time/residue: 1.8538 time to fit residues: 666.9051 Evaluate side-chains 355 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 328 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 71 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1683 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= 0.175 Angle : 0.447 5.643 21791 Z= 0.244 Chirality : 0.040 0.136 2299 Planarity : 0.003 0.033 2882 Dihedral : 3.833 17.173 2255 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.96 % Allowed : 11.82 % Favored : 86.22 % 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: 1.33 (0.19), residues: 2002 helix: 1.97 (0.19), residues: 770 sheet: 0.42 (0.24), residues: 495 loop : 0.16 (0.24), 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 K 36 ARG 0.004 0.000 ARG I 143 *********************** 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 325 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 1.749 Fit side-chains REVERT: B 77 GLU cc_start: 0.7293 (mp0) cc_final: 0.6698 (mp0) REVERT: B 78 MET cc_start: 0.8298 (tpp) cc_final: 0.7505 (tpp) REVERT: B 100 ASN cc_start: 0.7632 (t0) cc_final: 0.7347 (t0) REVERT: C 34 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: C 77 GLU cc_start: 0.7498 (mp0) cc_final: 0.7053 (mp0) REVERT: C 202 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6920 (tm-30) REVERT: D 78 MET cc_start: 0.8296 (tpt) cc_final: 0.8066 (tpt) REVERT: D 81 TYR cc_start: 0.8688 (p90) cc_final: 0.8315 (p90) REVERT: D 202 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6982 (tm-30) REVERT: E 76 ASN cc_start: 0.8414 (m-40) cc_final: 0.8152 (m-40) REVERT: E 197 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6633 (mm-30) REVERT: E 201 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: F 100 ASN cc_start: 0.7719 (t0) cc_final: 0.7425 (t0) REVERT: G 100 ASN cc_start: 0.7603 (t0) cc_final: 0.7314 (t0) REVERT: H 67 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6595 (mt-10) REVERT: H 100 ASN cc_start: 0.7755 (t0) cc_final: 0.7402 (t0) REVERT: H 202 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6505 (tm-30) REVERT: H 206 ASN cc_start: 0.7884 (m-40) cc_final: 0.7284 (m-40) REVERT: J 100 ASN cc_start: 0.7604 (t0) cc_final: 0.7329 (t0) REVERT: J 201 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: K 202 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7124 (tm-30) outliers start: 33 outliers final: 21 residues processed: 300 average time/residue: 1.8753 time to fit residues: 604.6364 Evaluate side-chains 311 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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 197 GLU Chi-restraints excluded: chain H residue 201 GLU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 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 159 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1692 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= 0.322 Angle : 0.491 7.630 21791 Z= 0.268 Chirality : 0.042 0.144 2299 Planarity : 0.003 0.041 2882 Dihedral : 3.901 16.495 2255 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.08 % Allowed : 12.24 % 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: 1.44 (0.19), residues: 2002 helix: 1.98 (0.19), residues: 770 sheet: 0.50 (0.24), residues: 495 loop : 0.31 (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 0.013 0.001 PHE D 26 TYR 0.013 0.002 TYR E 36 ARG 0.004 0.000 ARG C 193 *********************** 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 346 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 311 time to evaluate : 1.723 Fit side-chains REVERT: B 77 GLU cc_start: 0.7303 (mp0) cc_final: 0.6681 (mp0) REVERT: B 100 ASN cc_start: 0.7670 (t0) cc_final: 0.7438 (t0) REVERT: C 34 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: C 46 ARG cc_start: 0.7620 (mtt90) cc_final: 0.7376 (mtt-85) REVERT: C 77 GLU cc_start: 0.7535 (mp0) cc_final: 0.7043 (mp0) REVERT: C 197 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6808 (mt-10) REVERT: C 202 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6919 (tm-30) REVERT: D 78 MET cc_start: 0.8205 (tpt) cc_final: 0.7955 (tpt) REVERT: D 81 TYR cc_start: 0.8715 (p90) cc_final: 0.8355 (p90) REVERT: D 202 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6967 (tm-30) REVERT: E 76 ASN cc_start: 0.8458 (m-40) cc_final: 0.8203 (m-40) REVERT: E 194 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6858 (pt0) REVERT: E 197 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6663 (mm-30) REVERT: F 100 ASN cc_start: 0.7738 (t0) cc_final: 0.7453 (t0) REVERT: G 77 GLU cc_start: 0.7463 (mp0) cc_final: 0.7129 (mp0) REVERT: G 100 ASN cc_start: 0.7634 (t0) cc_final: 0.7349 (t0) REVERT: H 62 LYS cc_start: 0.8211 (tttt) cc_final: 0.7996 (tttt) REVERT: H 67 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6635 (mt-10) REVERT: H 100 ASN cc_start: 0.7771 (t0) cc_final: 0.7440 (t0) REVERT: H 202 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6513 (tm-30) REVERT: H 206 ASN cc_start: 0.7944 (m-40) cc_final: 0.7431 (m-40) REVERT: J 100 ASN cc_start: 0.7610 (t0) cc_final: 0.7337 (t0) REVERT: J 201 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: J 202 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7252 (tp30) REVERT: J 206 ASN cc_start: 0.8018 (m-40) cc_final: 0.7721 (m-40) REVERT: K 100 ASN cc_start: 0.7657 (t0) cc_final: 0.7280 (t0) REVERT: K 202 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7108 (tm-30) outliers start: 35 outliers final: 24 residues processed: 324 average time/residue: 1.8956 time to fit residues: 658.2925 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 : 1.791 ------------------------------------------------------------------------------- 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 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 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 64 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16214 Z= 0.233 Angle : 0.464 6.552 21791 Z= 0.253 Chirality : 0.040 0.172 2299 Planarity : 0.003 0.036 2882 Dihedral : 3.821 16.746 2255 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.44 % Allowed : 13.13 % Favored : 84.43 % 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: 1.67 (0.19), residues: 2002 helix: 2.13 (0.18), residues: 770 sheet: 0.61 (0.24), residues: 495 loop : 0.49 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 84 HIS 0.005 0.001 HIS A 86 PHE 0.009 0.001 PHE D 26 TYR 0.012 0.001 TYR E 36 ARG 0.010 0.000 ARG C 204 *********************** 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 354 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 1.881 Fit side-chains REVERT: B 77 GLU cc_start: 0.7320 (mp0) cc_final: 0.6755 (mp0) REVERT: B 100 ASN cc_start: 0.7641 (t0) cc_final: 0.7407 (t0) REVERT: C 34 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6787 (mm-30) REVERT: C 41 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8025 (mttp) REVERT: C 77 GLU cc_start: 0.7495 (mp0) cc_final: 0.7009 (mp0) REVERT: C 197 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6851 (mt-10) REVERT: C 202 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6940 (tm-30) REVERT: D 78 MET cc_start: 0.8140 (tpt) cc_final: 0.7895 (tpp) REVERT: D 81 TYR cc_start: 0.8706 (p90) cc_final: 0.8350 (p90) REVERT: D 202 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6960 (tm-30) REVERT: E 76 ASN cc_start: 0.8439 (m-40) cc_final: 0.8181 (m-40) REVERT: F 100 ASN cc_start: 0.7734 (t0) cc_final: 0.7446 (t0) REVERT: G 100 ASN cc_start: 0.7613 (t0) cc_final: 0.7332 (t0) REVERT: H 62 LYS cc_start: 0.8209 (tttt) cc_final: 0.8004 (tttt) REVERT: H 67 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6596 (mt-10) REVERT: H 100 ASN cc_start: 0.7761 (t0) cc_final: 0.7436 (t0) REVERT: H 202 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6501 (tm-30) REVERT: H 206 ASN cc_start: 0.7919 (m-40) cc_final: 0.7386 (m-40) REVERT: J 100 ASN cc_start: 0.7594 (t0) cc_final: 0.7326 (t0) REVERT: J 201 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: J 202 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7265 (tp30) REVERT: J 206 ASN cc_start: 0.8017 (m-40) cc_final: 0.7713 (m110) REVERT: K 77 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7152 (mm-30) REVERT: K 100 ASN cc_start: 0.7637 (t0) cc_final: 0.7269 (t0) REVERT: K 202 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7165 (tm-30) outliers start: 41 outliers final: 28 residues processed: 328 average time/residue: 1.8360 time to fit residues: 646.8853 Evaluate side-chains 343 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 312 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain 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 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 184 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 121 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 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16214 Z= 0.263 Angle : 0.474 8.902 21791 Z= 0.258 Chirality : 0.041 0.167 2299 Planarity : 0.003 0.044 2882 Dihedral : 3.820 16.580 2255 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.44 % Allowed : 13.78 % Favored : 83.78 % 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: 1.75 (0.19), residues: 2002 helix: 2.17 (0.18), residues: 770 sheet: 0.66 (0.24), residues: 495 loop : 0.58 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 84 HIS 0.005 0.002 HIS A 86 PHE 0.010 0.001 PHE D 26 TYR 0.014 0.002 TYR H 36 ARG 0.011 0.000 ARG C 204 *********************** 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 358 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 1.907 Fit side-chains REVERT: B 77 GLU cc_start: 0.7320 (mp0) cc_final: 0.6757 (mp0) REVERT: B 100 ASN cc_start: 0.7649 (t0) cc_final: 0.7419 (t0) REVERT: C 34 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6793 (mm-30) REVERT: C 41 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8028 (mttp) REVERT: C 77 GLU cc_start: 0.7505 (mp0) cc_final: 0.7040 (mp0) REVERT: C 197 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6819 (mt-10) REVERT: C 202 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6932 (tm-30) REVERT: D 78 MET cc_start: 0.8117 (tpt) cc_final: 0.7852 (tpt) REVERT: D 81 TYR cc_start: 0.8710 (p90) cc_final: 0.8350 (p90) REVERT: D 202 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6988 (tm-30) REVERT: E 76 ASN cc_start: 0.8453 (m-40) cc_final: 0.8193 (m-40) REVERT: F 100 ASN cc_start: 0.7741 (t0) cc_final: 0.7465 (t0) REVERT: G 100 ASN cc_start: 0.7616 (t0) cc_final: 0.7336 (t0) REVERT: H 62 LYS cc_start: 0.8211 (tttt) cc_final: 0.8006 (tttt) REVERT: H 67 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6604 (mt-10) REVERT: H 100 ASN cc_start: 0.7767 (t0) cc_final: 0.7463 (t0) REVERT: H 202 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6493 (tm-30) REVERT: H 206 ASN cc_start: 0.7926 (m-40) cc_final: 0.7382 (m-40) REVERT: J 100 ASN cc_start: 0.7595 (t0) cc_final: 0.7330 (t0) REVERT: J 201 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6232 (mp0) REVERT: J 202 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7261 (tp30) REVERT: J 206 ASN cc_start: 0.8044 (m-40) cc_final: 0.7703 (m110) REVERT: K 77 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7156 (mm-30) REVERT: K 100 ASN cc_start: 0.7645 (t0) cc_final: 0.7289 (t0) outliers start: 41 outliers final: 31 residues processed: 332 average time/residue: 1.9496 time to fit residues: 693.5417 Evaluate side-chains 351 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 317 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 41 LYS 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 E residue 132 LEU Chi-restraints excluded: chain E residue 176 ASN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN G 76 ASN G 176 ASN K 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16214 Z= 0.237 Angle : 0.471 8.076 21791 Z= 0.255 Chirality : 0.040 0.143 2299 Planarity : 0.003 0.050 2882 Dihedral : 3.787 16.648 2255 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.20 % Allowed : 14.50 % Favored : 83.30 % 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: 1.86 (0.19), residues: 2002 helix: 2.25 (0.18), residues: 770 sheet: 0.71 (0.24), residues: 495 loop : 0.66 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 K 36 ARG 0.012 0.000 ARG C 204 *********************** 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 350 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 1.828 Fit side-chains REVERT: B 77 GLU cc_start: 0.7313 (mp0) cc_final: 0.6791 (mp0) REVERT: B 100 ASN cc_start: 0.7631 (t0) cc_final: 0.7398 (t0) REVERT: C 34 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6775 (mm-30) REVERT: C 41 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8040 (mttp) REVERT: C 77 GLU cc_start: 0.7502 (mp0) cc_final: 0.7034 (mp0) REVERT: C 197 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6809 (mt-10) REVERT: C 202 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6928 (tm-30) REVERT: D 78 MET cc_start: 0.8078 (tpt) cc_final: 0.7805 (tpt) REVERT: D 81 TYR cc_start: 0.8703 (p90) cc_final: 0.8350 (p90) REVERT: D 202 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6989 (tm-30) REVERT: E 76 ASN cc_start: 0.8457 (m-40) cc_final: 0.8199 (m-40) REVERT: F 100 ASN cc_start: 0.7745 (t0) cc_final: 0.7472 (t0) REVERT: G 100 ASN cc_start: 0.7608 (t0) cc_final: 0.7327 (t0) REVERT: H 67 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6591 (mt-10) REVERT: H 100 ASN cc_start: 0.7770 (t0) cc_final: 0.7468 (t0) REVERT: H 202 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6483 (tm-30) REVERT: H 206 ASN cc_start: 0.7915 (m-40) cc_final: 0.7381 (m-40) REVERT: J 100 ASN cc_start: 0.7582 (t0) cc_final: 0.7317 (t0) REVERT: J 201 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: J 202 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7198 (tp30) REVERT: J 206 ASN cc_start: 0.8044 (m-40) cc_final: 0.7661 (m110) REVERT: K 100 ASN cc_start: 0.7645 (t0) cc_final: 0.7302 (t0) outliers start: 37 outliers final: 32 residues processed: 325 average time/residue: 1.9250 time to fit residues: 670.3498 Evaluate side-chains 346 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 311 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 A residue 201 GLU 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 41 LYS 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 E 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 166 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN G 76 ASN G 176 ASN K 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16214 Z= 0.167 Angle : 0.454 7.772 21791 Z= 0.245 Chirality : 0.039 0.152 2299 Planarity : 0.003 0.055 2882 Dihedral : 3.688 16.657 2255 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.14 % Allowed : 14.91 % 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: 2.01 (0.19), residues: 2002 helix: 2.37 (0.18), residues: 770 sheet: 0.80 (0.24), residues: 495 loop : 0.73 (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 0.012 0.001 TYR K 36 ARG 0.013 0.000 ARG C 204 *********************** 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 356 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 1.817 Fit side-chains REVERT: B 77 GLU cc_start: 0.7295 (mp0) cc_final: 0.6790 (mp0) REVERT: B 100 ASN cc_start: 0.7562 (t0) cc_final: 0.7344 (t0) REVERT: C 41 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8018 (mttp) REVERT: C 77 GLU cc_start: 0.7491 (mp0) cc_final: 0.7027 (mp0) REVERT: C 100 ASN cc_start: 0.7524 (t0) cc_final: 0.7192 (t0) REVERT: C 197 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6769 (mt-10) REVERT: C 202 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6905 (tm-30) REVERT: D 78 MET cc_start: 0.8053 (tpt) cc_final: 0.7771 (tpt) REVERT: D 81 TYR cc_start: 0.8681 (p90) cc_final: 0.8338 (p90) REVERT: D 202 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6854 (tm-30) REVERT: D 206 ASN cc_start: 0.7930 (m-40) cc_final: 0.7409 (m-40) REVERT: E 76 ASN cc_start: 0.8429 (m-40) cc_final: 0.8173 (m-40) REVERT: F 100 ASN cc_start: 0.7743 (t0) cc_final: 0.7473 (t0) REVERT: G 100 ASN cc_start: 0.7591 (t0) cc_final: 0.7314 (t0) REVERT: H 67 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6546 (mt-10) REVERT: H 100 ASN cc_start: 0.7780 (t0) cc_final: 0.7481 (t0) REVERT: H 202 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6476 (tm-30) REVERT: H 206 ASN cc_start: 0.7884 (m-40) cc_final: 0.7266 (m-40) REVERT: J 100 ASN cc_start: 0.7583 (t0) cc_final: 0.7317 (t0) REVERT: J 201 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: J 202 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7220 (tp30) REVERT: J 206 ASN cc_start: 0.8012 (m-40) cc_final: 0.7675 (m110) REVERT: K 100 ASN cc_start: 0.7637 (t0) cc_final: 0.7298 (t0) outliers start: 36 outliers final: 27 residues processed: 331 average time/residue: 1.9279 time to fit residues: 683.1491 Evaluate side-chains 347 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 318 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 56 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E 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 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 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 188 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 121 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16214 Z= 0.305 Angle : 0.496 7.655 21791 Z= 0.269 Chirality : 0.042 0.158 2299 Planarity : 0.003 0.060 2882 Dihedral : 3.805 17.269 2255 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.02 % Allowed : 15.39 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.19), residues: 2002 helix: 2.24 (0.18), residues: 770 sheet: 0.81 (0.24), residues: 495 loop : 0.72 (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 0.013 0.002 TYR K 36 ARG 0.014 0.000 ARG C 204 ********************** 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 345 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 311 time to evaluate : 1.737 Fit side-chains REVERT: B 77 GLU cc_start: 0.7305 (mp0) cc_final: 0.6798 (mp0) REVERT: B 100 ASN cc_start: 0.7655 (t0) cc_final: 0.7427 (t0) REVERT: C 41 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8046 (mttp) REVERT: C 77 GLU cc_start: 0.7517 (mp0) cc_final: 0.7014 (mp0) REVERT: C 100 ASN cc_start: 0.7565 (t0) cc_final: 0.7237 (t0) REVERT: C 197 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6815 (mt-10) REVERT: C 202 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6912 (tm-30) REVERT: D 81 TYR cc_start: 0.8710 (p90) cc_final: 0.8358 (p90) REVERT: D 202 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6977 (tm-30) REVERT: E 76 ASN cc_start: 0.8463 (m-40) cc_final: 0.8209 (m-40) REVERT: F 100 ASN cc_start: 0.7766 (t0) cc_final: 0.7500 (t0) REVERT: G 100 ASN cc_start: 0.7613 (t0) cc_final: 0.7333 (t0) REVERT: H 67 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6615 (mt-10) REVERT: H 100 ASN cc_start: 0.7803 (t0) cc_final: 0.7507 (t0) REVERT: H 202 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6505 (tm-30) REVERT: H 206 ASN cc_start: 0.7919 (m-40) cc_final: 0.7391 (m-40) REVERT: J 100 ASN cc_start: 0.7621 (t0) cc_final: 0.7355 (t0) REVERT: J 201 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: K 100 ASN cc_start: 0.7675 (t0) cc_final: 0.7343 (t0) outliers start: 34 outliers final: 27 residues processed: 323 average time/residue: 1.9565 time to fit residues: 677.2213 Evaluate side-chains 340 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 311 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 C residue 41 LYS Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain E 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 176 ASN ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 176 ASN G 76 ASN G 176 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.147427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.128337 restraints weight = 19846.214| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.75 r_work: 0.3661 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16214 Z= 0.233 Angle : 0.478 7.422 21791 Z= 0.259 Chirality : 0.040 0.149 2299 Planarity : 0.003 0.068 2882 Dihedral : 3.761 17.169 2255 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.90 % Allowed : 15.81 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.19), residues: 2002 helix: 2.32 (0.18), residues: 770 sheet: 0.83 (0.24), residues: 495 loop : 0.74 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 84 HIS 0.005 0.001 HIS C 86 PHE 0.009 0.001 PHE D 26 TYR 0.012 0.001 TYR E 36 ARG 0.013 0.000 ARG C 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8964.93 seconds wall clock time: 160 minutes 15.13 seconds (9615.13 seconds total)