Starting phenix.real_space_refine on Sun Jun 15 02:10:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jod_61659/06_2025/9jod_61659.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jod_61659/06_2025/9jod_61659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jod_61659/06_2025/9jod_61659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jod_61659/06_2025/9jod_61659.map" model { file = "/net/cci-nas-00/data/ceres_data/9jod_61659/06_2025/9jod_61659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jod_61659/06_2025/9jod_61659.cif" } resolution = 3.2 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= 0.017 sd= 1.764 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 77 5.16 5 C 10731 2.51 5 N 2863 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16849 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2407 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "B" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2407 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "C" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2407 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "D" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2407 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "E" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2407 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "F" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2407 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain: "G" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2407 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Time building chain proxies: 10.76, per 1000 atoms: 0.64 Number of scatterers: 16849 At special positions: 0 Unit cell: (180.88, 221.68, 77.52, 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 77 16.00 O 3178 8.00 N 2863 7.00 C 10731 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: 3.79 Conformation dependent library (CDL) restraints added in 2.2 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3892 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 39 sheets defined 23.8% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.553A pdb=" N LEU A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 100 through 110 removed outlier: 3.959A pdb=" N GLU A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 removed outlier: 3.572A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 234 through 247 Processing helix chain 'A' and resid 269 through 278 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 101 through 123 removed outlier: 3.834A pdb=" N GLN B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Proline residue: B 113 - end of helix removed outlier: 3.638A pdb=" N LYS B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 234 through 247 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.548A pdb=" N GLY B 253 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 254' Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 278 removed outlier: 3.611A pdb=" N ASN B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 100 through 110 Processing helix chain 'C' and resid 111 through 123 removed outlier: 3.692A pdb=" N GLU C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 234 through 247 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 278 removed outlier: 3.557A pdb=" N ASN C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 12 removed outlier: 3.532A pdb=" N LEU D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 101 through 123 removed outlier: 4.101A pdb=" N GLN D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Proline residue: D 113 - end of helix removed outlier: 3.604A pdb=" N LYS D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 121 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 270 through 278 removed outlier: 3.591A pdb=" N ASN D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 Processing helix chain 'E' and resid 29 through 32 Processing helix chain 'E' and resid 87 through 92 Processing helix chain 'E' and resid 101 through 123 removed outlier: 3.942A pdb=" N GLN E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) Proline residue: E 113 - end of helix removed outlier: 3.583A pdb=" N LEU E 121 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS E 122 " --> pdb=" O PHE E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 234 through 247 Processing helix chain 'E' and resid 269 through 278 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 101 through 111 Processing helix chain 'F' and resid 111 through 123 removed outlier: 3.771A pdb=" N GLU F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS F 119 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 121 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 234 through 246 Processing helix chain 'F' and resid 266 through 268 No H-bonds generated for 'chain 'F' and resid 266 through 268' Processing helix chain 'F' and resid 269 through 278 removed outlier: 3.538A pdb=" N LEU F 276 " --> pdb=" O ALA F 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 10 Processing helix chain 'G' and resid 87 through 92 Processing helix chain 'G' and resid 100 through 110 Processing helix chain 'G' and resid 111 through 123 removed outlier: 3.518A pdb=" N GLU G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 119 " --> pdb=" O GLU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 205 Processing helix chain 'G' and resid 234 through 246 Processing helix chain 'G' and resid 269 through 278 removed outlier: 3.697A pdb=" N ALA G 273 " --> pdb=" O LEU G 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 5.634A pdb=" N MET A 35 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU A 185 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 37 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ARG A 187 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG A 215 " --> pdb=" O ARG A 186 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS A 188 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 213 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU A 190 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY A 211 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 192 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 209 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ARG A 194 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU A 207 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 49 removed outlier: 3.577A pdb=" N TRP A 48 " --> pdb=" O HIS A 70 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N MET A 67 " --> pdb=" O VAL B 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 160 removed outlier: 6.647A pdb=" N VAL A 159 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 263 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA A 302 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A 265 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 16 removed outlier: 6.294A pdb=" N SER B 14 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY C 47 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ARG B 16 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N LEU C 49 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 38 removed outlier: 5.880A pdb=" N MET B 35 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU B 185 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 37 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ARG B 187 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG B 215 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS B 188 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B 213 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 190 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 211 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 192 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 209 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ARG B 194 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU B 207 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 38 removed outlier: 5.880A pdb=" N MET B 35 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU B 185 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 37 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ARG B 187 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG B 215 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS B 188 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B 213 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 190 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 211 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 192 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 209 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ARG B 194 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU B 207 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N GLN C 65 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 82 " --> pdb=" O GLN C 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 75 removed outlier: 6.810A pdb=" N SER B 43 " --> pdb=" O SER G 14 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ARG G 16 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 45 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.605A pdb=" N GLY G 84 " --> pdb=" O GLN B 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.674A pdb=" N LYS G 77 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLU G 207 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG G 194 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU G 209 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL G 192 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY G 211 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU G 190 " --> pdb=" O GLY G 211 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N SER G 213 " --> pdb=" O LYS G 188 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS G 188 " --> pdb=" O SER G 213 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ARG G 215 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET G 35 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLU G 185 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL G 37 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ARG G 187 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 160 removed outlier: 7.135A pdb=" N VAL B 159 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 263 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AB4, first strand: chain 'C' and resid 13 through 16 removed outlier: 6.052A pdb=" N SER C 14 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY D 47 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ARG C 16 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N LEU D 49 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.126A pdb=" N MET C 35 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLU C 185 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 37 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ARG C 187 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG C 215 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS C 188 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER C 213 " --> pdb=" O LYS C 188 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU C 190 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY C 211 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 192 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 209 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG C 194 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS C 77 " --> pdb=" O ARG C 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.126A pdb=" N MET C 35 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLU C 185 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 37 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ARG C 187 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG C 215 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS C 188 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER C 213 " --> pdb=" O LYS C 188 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU C 190 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY C 211 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 192 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 209 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG C 194 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS C 77 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N GLN D 65 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 82 " --> pdb=" O GLN D 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 160 removed outlier: 6.648A pdb=" N VAL C 159 " --> pdb=" O LYS C 230 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 281 through 283 Processing sheet with id=AC1, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.203A pdb=" N SER D 14 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY E 47 " --> pdb=" O SER D 14 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ARG D 16 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N LEU E 49 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP E 48 " --> pdb=" O HIS E 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 34 through 38 removed outlier: 5.763A pdb=" N MET D 35 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU D 185 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 37 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ARG D 187 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG D 215 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS D 188 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER D 213 " --> pdb=" O LYS D 188 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU D 190 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY D 211 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 192 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU D 209 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG D 194 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU D 207 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 77 " --> pdb=" O ARG D 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 34 through 38 removed outlier: 5.763A pdb=" N MET D 35 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU D 185 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 37 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ARG D 187 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG D 215 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS D 188 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER D 213 " --> pdb=" O LYS D 188 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU D 190 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY D 211 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 192 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU D 209 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARG D 194 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU D 207 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 77 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N GLN E 65 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR D 82 " --> pdb=" O GLN E 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AC5, first strand: chain 'D' and resid 158 through 160 removed outlier: 6.878A pdb=" N VAL D 159 " --> pdb=" O LYS D 230 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE D 263 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA D 302 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 265 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 249 through 250 removed outlier: 3.760A pdb=" N LYS D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 281 through 284 removed outlier: 3.630A pdb=" N THR D 287 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 13 through 15 removed outlier: 5.805A pdb=" N SER E 14 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY F 47 " --> pdb=" O SER E 14 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 34 through 38 removed outlier: 5.851A pdb=" N MET E 35 " --> pdb=" O PHE E 183 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU E 185 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL E 37 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ARG E 187 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLN E 184 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N GLY E 219 " --> pdb=" O GLN E 184 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG E 186 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N ALA E 217 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS E 188 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG E 215 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 209 " --> pdb=" O ARG E 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 34 through 38 removed outlier: 5.851A pdb=" N MET E 35 " --> pdb=" O PHE E 183 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU E 185 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL E 37 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ARG E 187 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLN E 184 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N GLY E 219 " --> pdb=" O GLN E 184 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG E 186 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N ALA E 217 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS E 188 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG E 215 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 209 " --> pdb=" O ARG E 194 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AD3, first strand: chain 'E' and resid 158 through 160 removed outlier: 6.461A pdb=" N VAL E 159 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE E 263 " --> pdb=" O VAL E 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 281 through 283 Processing sheet with id=AD5, first strand: chain 'F' and resid 14 through 15 removed outlier: 5.850A pdb=" N SER F 14 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLY G 47 " --> pdb=" O SER F 14 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP G 48 " --> pdb=" O HIS G 70 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS G 70 " --> pdb=" O TRP G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 34 through 38 removed outlier: 6.143A pdb=" N MET F 35 " --> pdb=" O PHE F 183 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLU F 185 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL F 37 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ARG F 187 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN F 184 " --> pdb=" O GLY F 219 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY F 219 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG F 186 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ALA F 217 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS F 188 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ARG F 215 " --> pdb=" O LYS F 188 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 209 " --> pdb=" O ARG F 194 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AD8, first strand: chain 'F' and resid 158 through 160 removed outlier: 6.822A pdb=" N VAL F 159 " --> pdb=" O LYS F 230 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 281 through 284 removed outlier: 3.877A pdb=" N THR F 287 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AE2, first strand: chain 'G' and resid 158 through 160 removed outlier: 6.928A pdb=" N VAL G 159 " --> pdb=" O LYS G 230 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 281 through 283 565 hydrogen bonds defined for protein. 1575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2971 1.32 - 1.44: 4526 1.44 - 1.56: 9597 1.56 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 17234 Sorted by residual: bond pdb=" CA SER B 151 " pdb=" CB SER B 151 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.38e-02 5.25e+03 1.38e+01 bond pdb=" N LEU G 120 " pdb=" CA LEU G 120 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.17e-02 7.31e+03 1.13e+01 bond pdb=" CG HIS G 140 " pdb=" CD2 HIS G 140 " ideal model delta sigma weight residual 1.354 1.320 0.034 1.10e-02 8.26e+03 9.34e+00 bond pdb=" CA SER F 151 " pdb=" CB SER F 151 " ideal model delta sigma weight residual 1.528 1.488 0.040 1.35e-02 5.49e+03 8.70e+00 bond pdb=" N LEU C 120 " pdb=" CA LEU C 120 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.62e+00 ... (remaining 17229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 22615 1.81 - 3.62: 588 3.62 - 5.43: 87 5.43 - 7.23: 9 7.23 - 9.04: 4 Bond angle restraints: 23303 Sorted by residual: angle pdb=" N LEU A 120 " pdb=" CA LEU A 120 " pdb=" C LEU A 120 " ideal model delta sigma weight residual 112.68 103.89 8.79 1.33e+00 5.65e-01 4.37e+01 angle pdb=" N LYS E 119 " pdb=" CA LYS E 119 " pdb=" C LYS E 119 " ideal model delta sigma weight residual 113.97 105.83 8.14 1.28e+00 6.10e-01 4.04e+01 angle pdb=" CA GLY D 150 " pdb=" C GLY D 150 " pdb=" O GLY D 150 " ideal model delta sigma weight residual 122.45 118.37 4.08 7.20e-01 1.93e+00 3.21e+01 angle pdb=" C LYS E 122 " pdb=" N ASP E 123 " pdb=" CA ASP E 123 " ideal model delta sigma weight residual 123.25 114.21 9.04 1.69e+00 3.50e-01 2.86e+01 angle pdb=" C LYS C 122 " pdb=" N ASP C 123 " pdb=" CA ASP C 123 " ideal model delta sigma weight residual 122.24 114.77 7.47 1.46e+00 4.69e-01 2.62e+01 ... (remaining 23298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9013 17.99 - 35.97: 928 35.97 - 53.96: 197 53.96 - 71.94: 81 71.94 - 89.93: 8 Dihedral angle restraints: 10227 sinusoidal: 4144 harmonic: 6083 Sorted by residual: dihedral pdb=" CA THR F 149 " pdb=" C THR F 149 " pdb=" N GLY F 150 " pdb=" CA GLY F 150 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLY G 219 " pdb=" C GLY G 219 " pdb=" N TYR G 220 " pdb=" CA TYR G 220 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA VAL F 111 " pdb=" C VAL F 111 " pdb=" N GLN F 112 " pdb=" CA GLN F 112 " ideal model delta harmonic sigma weight residual 180.00 -163.48 -16.52 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 10224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1964 0.053 - 0.105: 411 0.105 - 0.158: 100 0.158 - 0.211: 11 0.211 - 0.264: 6 Chirality restraints: 2492 Sorted by residual: chirality pdb=" CA LEU A 120 " pdb=" N LEU A 120 " pdb=" C LEU A 120 " pdb=" CB LEU A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA LEU E 121 " pdb=" N LEU E 121 " pdb=" C LEU E 121 " pdb=" CB LEU E 121 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA LEU F 120 " pdb=" N LEU F 120 " pdb=" C LEU F 120 " pdb=" CB LEU F 120 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2489 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 119 " 0.024 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C LYS C 119 " -0.081 2.00e-02 2.50e+03 pdb=" O LYS C 119 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU C 120 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 118 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C PHE B 118 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE B 118 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS B 119 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 119 " 0.019 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C LYS G 119 " -0.063 2.00e-02 2.50e+03 pdb=" O LYS G 119 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU G 120 " 0.021 2.00e-02 2.50e+03 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1773 2.75 - 3.28: 14728 3.28 - 3.82: 25541 3.82 - 4.36: 31741 4.36 - 4.90: 57242 Nonbonded interactions: 131025 Sorted by model distance: nonbonded pdb=" OG SER B 14 " pdb=" OD1 ASN C 44 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLU C 24 " pdb=" NH1 ARG D 176 " model vdw 2.241 3.120 nonbonded pdb=" OE1 GLU F 104 " pdb=" NH2 ARG F 107 " model vdw 2.256 3.120 nonbonded pdb=" NH1 ARG A 186 " pdb=" OD1 ASP B 92 " model vdw 2.263 3.120 nonbonded pdb=" OG1 THR G 41 " pdb=" N ARG G 42 " model vdw 2.271 3.120 ... (remaining 131020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.440 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 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 : 0.005 0.051 17234 Z= 0.255 Angle : 0.686 9.042 23303 Z= 0.428 Chirality : 0.048 0.264 2492 Planarity : 0.005 0.047 3045 Dihedral : 15.830 89.927 6335 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.39 % Allowed : 16.51 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2121 helix: -0.98 (0.24), residues: 484 sheet: 0.23 (0.23), residues: 505 loop : -1.44 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 223 HIS 0.008 0.002 HIS E 140 PHE 0.023 0.002 PHE B 19 TYR 0.014 0.001 TYR E 98 ARG 0.007 0.001 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.19671 ( 505) hydrogen bonds : angle 8.62859 ( 1575) covalent geometry : bond 0.00492 (17234) covalent geometry : angle 0.68639 (23303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 1.853 Fit side-chains REVERT: B 12 MET cc_start: 0.9134 (mtt) cc_final: 0.8872 (mtp) REVERT: C 196 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7930 (mtp-110) REVERT: E 198 ASP cc_start: 0.7643 (t0) cc_final: 0.7427 (t70) REVERT: G 198 ASP cc_start: 0.6902 (t0) cc_final: 0.6633 (t0) outliers start: 25 outliers final: 3 residues processed: 262 average time/residue: 0.3436 time to fit residues: 126.8683 Evaluate side-chains 177 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain F residue 122 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 164 optimal weight: 0.0010 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 161 GLN B 157 ASN C 157 ASN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.092371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.073424 restraints weight = 27080.677| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 1.54 r_work: 0.2566 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17234 Z= 0.150 Angle : 0.526 6.813 23303 Z= 0.281 Chirality : 0.043 0.154 2492 Planarity : 0.005 0.041 3045 Dihedral : 4.270 24.217 2297 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.28 % Allowed : 15.12 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2121 helix: -0.50 (0.25), residues: 490 sheet: 0.45 (0.23), residues: 493 loop : -1.23 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 48 HIS 0.004 0.001 HIS G 262 PHE 0.022 0.002 PHE F 282 TYR 0.011 0.001 TYR B 143 ARG 0.006 0.001 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 505) hydrogen bonds : angle 5.66338 ( 1575) covalent geometry : bond 0.00355 (17234) covalent geometry : angle 0.52551 (23303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 1.908 Fit side-chains REVERT: A 184 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: B 12 MET cc_start: 0.9114 (mtt) cc_final: 0.8831 (mtp) REVERT: B 122 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8849 (ttpp) REVERT: B 233 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9138 (tt) REVERT: C 196 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.8090 (mtp-110) REVERT: D 188 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8511 (mmtt) REVERT: D 199 ASP cc_start: 0.8405 (m-30) cc_final: 0.7938 (m-30) REVERT: E 61 LYS cc_start: 0.5872 (tptt) cc_final: 0.5625 (tptt) REVERT: E 204 MET cc_start: 0.8982 (tpt) cc_final: 0.8761 (tpt) REVERT: F 41 THR cc_start: 0.9511 (t) cc_final: 0.9269 (m) REVERT: F 107 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8555 (mtm-85) REVERT: F 225 MET cc_start: 0.9411 (mtm) cc_final: 0.9182 (mtm) REVERT: G 198 ASP cc_start: 0.7582 (t0) cc_final: 0.7211 (t0) REVERT: G 267 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9076 (p) outliers start: 41 outliers final: 19 residues processed: 214 average time/residue: 0.3150 time to fit residues: 98.3150 Evaluate side-chains 188 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 23 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN D 29 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN G 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.088623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.069443 restraints weight = 27302.105| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 1.57 r_work: 0.2487 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 17234 Z= 0.282 Angle : 0.635 9.087 23303 Z= 0.334 Chirality : 0.048 0.236 2492 Planarity : 0.006 0.071 3045 Dihedral : 4.716 25.135 2289 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.17 % Allowed : 16.18 % Favored : 80.66 % 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: -1.01 (0.17), residues: 2121 helix: -0.42 (0.25), residues: 465 sheet: 0.35 (0.23), residues: 499 loop : -1.23 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 15 HIS 0.004 0.001 HIS G 201 PHE 0.034 0.002 PHE C 282 TYR 0.015 0.002 TYR B 143 ARG 0.007 0.001 ARG G 215 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 505) hydrogen bonds : angle 5.71308 ( 1575) covalent geometry : bond 0.00686 (17234) covalent geometry : angle 0.63461 (23303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 1.855 Fit side-chains REVERT: A 139 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: B 2 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8628 (mm) REVERT: B 12 MET cc_start: 0.9167 (mtt) cc_final: 0.8904 (mtt) REVERT: B 233 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9094 (tt) REVERT: C 107 ARG cc_start: 0.8748 (mtm-85) cc_final: 0.8482 (mtt90) REVERT: F 225 MET cc_start: 0.9436 (mtm) cc_final: 0.9212 (mtm) REVERT: G 198 ASP cc_start: 0.7613 (t0) cc_final: 0.7240 (t0) outliers start: 57 outliers final: 40 residues processed: 213 average time/residue: 0.3022 time to fit residues: 94.6708 Evaluate side-chains 197 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 201 HIS Chi-restraints excluded: chain G residue 267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 12 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 194 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.072483 restraints weight = 27093.944| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 1.56 r_work: 0.2548 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17234 Z= 0.121 Angle : 0.495 6.701 23303 Z= 0.263 Chirality : 0.042 0.145 2492 Planarity : 0.004 0.039 3045 Dihedral : 4.224 22.022 2289 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.61 % Allowed : 16.68 % Favored : 80.71 % 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: -0.78 (0.17), residues: 2121 helix: -0.09 (0.25), residues: 489 sheet: 0.36 (0.22), residues: 501 loop : -1.12 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 48 HIS 0.003 0.001 HIS D 70 PHE 0.021 0.001 PHE C 282 TYR 0.009 0.001 TYR E 98 ARG 0.005 0.000 ARG G 196 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 505) hydrogen bonds : angle 5.21382 ( 1575) covalent geometry : bond 0.00284 (17234) covalent geometry : angle 0.49546 (23303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 1.934 Fit side-chains REVERT: A 20 GLN cc_start: 0.8242 (pt0) cc_final: 0.7849 (pm20) REVERT: A 65 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8426 (mm-40) REVERT: A 139 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: B 2 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8577 (mm) REVERT: B 12 MET cc_start: 0.9145 (mtt) cc_final: 0.8876 (mtt) REVERT: B 122 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8891 (ttpp) REVERT: C 256 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8700 (mt) REVERT: C 305 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7870 (tt) REVERT: D 188 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8464 (mmtt) REVERT: F 165 SER cc_start: 0.8943 (m) cc_final: 0.8649 (p) REVERT: F 225 MET cc_start: 0.9425 (mtm) cc_final: 0.9192 (mtm) REVERT: G 198 ASP cc_start: 0.7634 (t0) cc_final: 0.7243 (t0) REVERT: G 267 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9084 (p) outliers start: 47 outliers final: 26 residues processed: 209 average time/residue: 0.3161 time to fit residues: 97.1961 Evaluate side-chains 188 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 201 HIS Chi-restraints excluded: chain G residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 69 optimal weight: 0.0670 chunk 103 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.092009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.072729 restraints weight = 27230.254| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 1.59 r_work: 0.2552 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17234 Z= 0.116 Angle : 0.486 6.604 23303 Z= 0.258 Chirality : 0.042 0.133 2492 Planarity : 0.004 0.035 3045 Dihedral : 4.080 20.782 2289 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.33 % Allowed : 17.23 % Favored : 80.43 % 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: -0.65 (0.18), residues: 2121 helix: 0.17 (0.26), residues: 469 sheet: 0.38 (0.22), residues: 501 loop : -1.06 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 48 HIS 0.003 0.001 HIS D 70 PHE 0.020 0.001 PHE C 282 TYR 0.008 0.001 TYR B 72 ARG 0.006 0.000 ARG G 196 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 505) hydrogen bonds : angle 5.04570 ( 1575) covalent geometry : bond 0.00272 (17234) covalent geometry : angle 0.48618 (23303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.850 Fit side-chains REVERT: A 139 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: B 2 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8570 (mm) REVERT: B 12 MET cc_start: 0.9127 (mtt) cc_final: 0.8861 (mtt) REVERT: B 122 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8818 (ttpp) REVERT: C 151 SER cc_start: 0.9076 (m) cc_final: 0.8874 (p) REVERT: C 256 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8690 (mt) REVERT: C 305 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7569 (tt) REVERT: D 188 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8479 (mmtt) REVERT: F 165 SER cc_start: 0.8960 (m) cc_final: 0.8660 (p) REVERT: F 225 MET cc_start: 0.9431 (mtm) cc_final: 0.9200 (mtm) REVERT: G 198 ASP cc_start: 0.7627 (t0) cc_final: 0.7274 (t0) REVERT: G 267 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9053 (p) outliers start: 42 outliers final: 31 residues processed: 203 average time/residue: 0.2978 time to fit residues: 89.4556 Evaluate side-chains 196 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 201 HIS Chi-restraints excluded: chain G residue 267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 26 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 184 optimal weight: 0.0030 chunk 49 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.092066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.072698 restraints weight = 27202.447| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 1.59 r_work: 0.2554 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17234 Z= 0.116 Angle : 0.484 6.622 23303 Z= 0.256 Chirality : 0.042 0.133 2492 Planarity : 0.004 0.034 3045 Dihedral : 3.986 19.801 2289 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.67 % Allowed : 16.90 % Favored : 80.43 % 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: -0.57 (0.18), residues: 2121 helix: 0.26 (0.26), residues: 469 sheet: 0.36 (0.22), residues: 511 loop : -0.99 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 48 HIS 0.003 0.001 HIS D 70 PHE 0.020 0.001 PHE C 282 TYR 0.009 0.001 TYR C 143 ARG 0.007 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 505) hydrogen bonds : angle 4.94306 ( 1575) covalent geometry : bond 0.00272 (17234) covalent geometry : angle 0.48373 (23303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 2.001 Fit side-chains REVERT: A 20 GLN cc_start: 0.8219 (pt0) cc_final: 0.7932 (pm20) REVERT: A 65 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8430 (mm-40) REVERT: A 139 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: A 184 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: B 2 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8548 (mm) REVERT: B 12 MET cc_start: 0.9122 (mtt) cc_final: 0.8848 (mtt) REVERT: B 122 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8820 (ttpp) REVERT: C 256 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8683 (mt) REVERT: C 305 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7347 (tt) REVERT: F 165 SER cc_start: 0.8961 (m) cc_final: 0.8659 (p) REVERT: F 225 MET cc_start: 0.9425 (mtm) cc_final: 0.9187 (mtm) REVERT: G 198 ASP cc_start: 0.7668 (t0) cc_final: 0.7306 (t0) REVERT: G 267 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9063 (p) outliers start: 48 outliers final: 34 residues processed: 206 average time/residue: 0.3019 time to fit residues: 92.8587 Evaluate side-chains 201 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 194 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.090278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.070929 restraints weight = 27060.739| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 1.55 r_work: 0.2518 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2409 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17234 Z= 0.175 Angle : 0.534 7.976 23303 Z= 0.281 Chirality : 0.044 0.140 2492 Planarity : 0.004 0.041 3045 Dihedral : 4.277 22.319 2289 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.78 % Allowed : 16.95 % Favored : 80.27 % 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: -0.63 (0.18), residues: 2121 helix: 0.19 (0.26), residues: 465 sheet: 0.34 (0.22), residues: 511 loop : -1.01 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 48 HIS 0.003 0.001 HIS F 70 PHE 0.027 0.002 PHE C 282 TYR 0.010 0.001 TYR C 143 ARG 0.006 0.001 ARG E 176 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 505) hydrogen bonds : angle 5.14393 ( 1575) covalent geometry : bond 0.00422 (17234) covalent geometry : angle 0.53387 (23303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 2.074 Fit side-chains REVERT: A 65 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8479 (mm-40) REVERT: A 107 ARG cc_start: 0.8966 (mtt90) cc_final: 0.8751 (mmm-85) REVERT: A 139 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: A 184 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8599 (tt0) REVERT: B 2 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8620 (mm) REVERT: B 12 MET cc_start: 0.9192 (mtt) cc_final: 0.8924 (mtt) REVERT: B 122 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8890 (ttpp) REVERT: C 256 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8728 (mt) REVERT: C 305 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7889 (tt) REVERT: F 107 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8530 (mtm110) REVERT: F 165 SER cc_start: 0.8963 (m) cc_final: 0.8680 (p) REVERT: F 225 MET cc_start: 0.9419 (mtm) cc_final: 0.9204 (mtm) REVERT: G 198 ASP cc_start: 0.7831 (t0) cc_final: 0.7429 (t0) REVERT: G 267 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9078 (p) outliers start: 50 outliers final: 35 residues processed: 200 average time/residue: 0.3232 time to fit residues: 96.6606 Evaluate side-chains 193 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 205 optimal weight: 0.0370 chunk 28 optimal weight: 30.0000 chunk 105 optimal weight: 0.0060 chunk 129 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 184 GLN F 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.073389 restraints weight = 26923.925| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 1.56 r_work: 0.2568 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17234 Z= 0.101 Angle : 0.470 6.347 23303 Z= 0.249 Chirality : 0.041 0.130 2492 Planarity : 0.004 0.035 3045 Dihedral : 3.922 19.380 2289 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.28 % Allowed : 17.45 % Favored : 80.27 % 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: -0.50 (0.18), residues: 2121 helix: 0.35 (0.26), residues: 469 sheet: 0.39 (0.22), residues: 521 loop : -0.96 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 48 HIS 0.002 0.001 HIS D 70 PHE 0.018 0.001 PHE C 282 TYR 0.008 0.001 TYR B 72 ARG 0.007 0.000 ARG G 196 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 505) hydrogen bonds : angle 4.85876 ( 1575) covalent geometry : bond 0.00235 (17234) covalent geometry : angle 0.46959 (23303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 2.086 Fit side-chains REVERT: A 20 GLN cc_start: 0.8215 (pt0) cc_final: 0.7943 (pm20) REVERT: A 65 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8444 (mm-40) REVERT: A 107 ARG cc_start: 0.8896 (mtt90) cc_final: 0.8656 (mtp85) REVERT: A 139 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: A 184 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: B 2 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8533 (mm) REVERT: B 12 MET cc_start: 0.9147 (mtt) cc_final: 0.8876 (mtt) REVERT: B 122 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8800 (ttpp) REVERT: C 256 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8684 (mt) REVERT: C 305 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7359 (tt) REVERT: D 176 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7831 (mtt180) REVERT: F 165 SER cc_start: 0.8954 (m) cc_final: 0.8665 (p) REVERT: F 225 MET cc_start: 0.9408 (mtm) cc_final: 0.9192 (mtm) REVERT: G 198 ASP cc_start: 0.7797 (t0) cc_final: 0.7385 (t0) outliers start: 41 outliers final: 30 residues processed: 193 average time/residue: 0.3151 time to fit residues: 90.3136 Evaluate side-chains 192 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 282 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 74 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.092238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.072972 restraints weight = 27124.259| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 1.55 r_work: 0.2556 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17234 Z= 0.117 Angle : 0.486 6.731 23303 Z= 0.257 Chirality : 0.042 0.133 2492 Planarity : 0.004 0.034 3045 Dihedral : 3.951 19.222 2289 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.06 % Allowed : 17.90 % Favored : 80.04 % 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: -0.48 (0.18), residues: 2121 helix: 0.34 (0.26), residues: 470 sheet: 0.39 (0.22), residues: 511 loop : -0.92 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 48 HIS 0.002 0.001 HIS D 70 PHE 0.020 0.001 PHE C 282 TYR 0.008 0.001 TYR B 72 ARG 0.008 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.03024 ( 505) hydrogen bonds : angle 4.87603 ( 1575) covalent geometry : bond 0.00278 (17234) covalent geometry : angle 0.48642 (23303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 2.029 Fit side-chains REVERT: A 20 GLN cc_start: 0.8225 (pt0) cc_final: 0.7961 (pm20) REVERT: A 65 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8457 (mm-40) REVERT: A 107 ARG cc_start: 0.8936 (mtt90) cc_final: 0.8707 (mtp85) REVERT: A 139 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: A 184 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: B 2 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8531 (mm) REVERT: B 4 THR cc_start: 0.9320 (p) cc_final: 0.9017 (m) REVERT: B 12 MET cc_start: 0.9185 (mtt) cc_final: 0.8915 (mtt) REVERT: B 122 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8808 (ttpp) REVERT: C 256 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8699 (mt) REVERT: C 305 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7358 (tt) REVERT: F 165 SER cc_start: 0.8947 (m) cc_final: 0.8670 (p) REVERT: F 225 MET cc_start: 0.9387 (mtm) cc_final: 0.9173 (mtm) REVERT: G 198 ASP cc_start: 0.7860 (t0) cc_final: 0.7444 (t0) REVERT: G 267 VAL cc_start: 0.9388 (OUTLIER) cc_final: 0.9086 (p) outliers start: 37 outliers final: 29 residues processed: 190 average time/residue: 0.3120 time to fit residues: 87.9488 Evaluate side-chains 195 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 164 optimal weight: 0.0570 chunk 65 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.073429 restraints weight = 27018.683| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 1.55 r_work: 0.2564 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17234 Z= 0.111 Angle : 0.477 6.539 23303 Z= 0.252 Chirality : 0.042 0.132 2492 Planarity : 0.004 0.035 3045 Dihedral : 3.904 18.756 2289 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.11 % Allowed : 17.84 % Favored : 80.04 % 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: -0.44 (0.18), residues: 2121 helix: 0.38 (0.26), residues: 471 sheet: 0.41 (0.22), residues: 511 loop : -0.89 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 48 HIS 0.002 0.001 HIS D 70 PHE 0.018 0.001 PHE C 282 TYR 0.008 0.001 TYR B 72 ARG 0.008 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 505) hydrogen bonds : angle 4.83406 ( 1575) covalent geometry : bond 0.00261 (17234) covalent geometry : angle 0.47721 (23303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.927 Fit side-chains REVERT: A 1 MET cc_start: 0.7583 (tmm) cc_final: 0.7177 (tpp) REVERT: A 20 GLN cc_start: 0.8192 (pt0) cc_final: 0.7964 (pm20) REVERT: A 65 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: A 107 ARG cc_start: 0.8929 (mtt90) cc_final: 0.8712 (mtp85) REVERT: A 139 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: A 184 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: B 2 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8512 (mm) REVERT: B 4 THR cc_start: 0.9291 (p) cc_final: 0.9005 (m) REVERT: B 12 MET cc_start: 0.9178 (mtt) cc_final: 0.8909 (mtt) REVERT: B 122 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8809 (ttpp) REVERT: C 256 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8690 (mt) REVERT: C 305 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7282 (tt) REVERT: D 204 MET cc_start: 0.8751 (mmm) cc_final: 0.8193 (mmm) REVERT: F 165 SER cc_start: 0.8945 (m) cc_final: 0.8671 (p) REVERT: F 225 MET cc_start: 0.9383 (mtm) cc_final: 0.9164 (mtm) REVERT: G 198 ASP cc_start: 0.7869 (t0) cc_final: 0.7452 (t0) REVERT: G 267 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9071 (p) outliers start: 38 outliers final: 30 residues processed: 194 average time/residue: 0.3036 time to fit residues: 87.4474 Evaluate side-chains 193 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 1 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.091672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.072453 restraints weight = 26924.066| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 1.54 r_work: 0.2546 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17234 Z= 0.132 Angle : 0.497 7.202 23303 Z= 0.262 Chirality : 0.042 0.133 2492 Planarity : 0.004 0.038 3045 Dihedral : 4.031 19.972 2289 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.17 % Allowed : 17.84 % Favored : 79.99 % 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: -0.48 (0.18), residues: 2121 helix: 0.32 (0.26), residues: 471 sheet: 0.38 (0.22), residues: 511 loop : -0.91 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 48 HIS 0.002 0.001 HIS D 70 PHE 0.022 0.001 PHE C 282 TYR 0.009 0.001 TYR E 98 ARG 0.008 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 505) hydrogen bonds : angle 4.91341 ( 1575) covalent geometry : bond 0.00314 (17234) covalent geometry : angle 0.49708 (23303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8788.33 seconds wall clock time: 150 minutes 45.51 seconds (9045.51 seconds total)