Starting phenix.real_space_refine on Fri May 16 19:37:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2d_44104/05_2025/9b2d_44104_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2d_44104/05_2025/9b2d_44104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2d_44104/05_2025/9b2d_44104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2d_44104/05_2025/9b2d_44104.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2d_44104/05_2025/9b2d_44104_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2d_44104/05_2025/9b2d_44104_trim.cif" } resolution = 2.4 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= 0.001 sd= 0.040 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: 8 Type Number sf(0) Gaussians Al 6 5.89 5 P 36 5.49 5 Mg 6 5.21 5 S 102 5.16 5 C 9150 2.51 5 N 2586 2.21 5 O 2862 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14766 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "E" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "F" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain breaks: 1 Chain: "K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 480 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.01, per 1000 atoms: 0.68 Number of scatterers: 14766 At special positions: 0 Unit cell: (114.92, 113.56, 166.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 36 15.00 Al 6 13.00 Mg 6 11.99 F 18 9.00 O 2862 8.00 N 2586 7.00 C 9150 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 18 sheets defined 50.9% alpha, 16.5% beta 0 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.806A pdb=" N LEU C 86 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.584A pdb=" N VAL C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.555A pdb=" N VAL C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 127 through 140 removed outlier: 3.921A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 164 through 172 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.518A pdb=" N LEU C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 204 No H-bonds generated for 'chain 'C' and resid 203 through 204' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.620A pdb=" N ILE C 208 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 236 removed outlier: 3.922A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 254 through 270 removed outlier: 4.301A pdb=" N LEU C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 removed outlier: 4.377A pdb=" N THR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.736A pdb=" N MET C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.567A pdb=" N VAL D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 128 through 140 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.523A pdb=" N SER D 155 " --> pdb=" O HIS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 171 Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.576A pdb=" N LEU D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.520A pdb=" N ILE D 208 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 236 removed outlier: 4.131A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 254 through 270 removed outlier: 4.168A pdb=" N LEU D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 removed outlier: 4.392A pdb=" N THR D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 318 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.645A pdb=" N MET D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 354 " --> pdb=" O MET D 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.599A pdb=" N LEU E 86 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 103 removed outlier: 3.796A pdb=" N VAL E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 removed outlier: 3.524A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 125 through 140 removed outlier: 3.557A pdb=" N ALA E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 164 through 172 Processing helix chain 'E' and resid 190 through 202 removed outlier: 3.553A pdb=" N LEU E 194 " --> pdb=" O GLY E 190 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL E 200 " --> pdb=" O HIS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 204 No H-bonds generated for 'chain 'E' and resid 203 through 204' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 225 through 236 removed outlier: 3.810A pdb=" N LEU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 254 through 270 removed outlier: 4.188A pdb=" N LEU E 262 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 270 " --> pdb=" O ALA E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 removed outlier: 4.312A pdb=" N THR E 288 " --> pdb=" O ALA E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 318 Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.541A pdb=" N MET E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 92 through 103 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.538A pdb=" N VAL F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 164 through 172 Processing helix chain 'F' and resid 190 through 202 removed outlier: 3.547A pdb=" N LEU F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 200 " --> pdb=" O HIS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 204 No H-bonds generated for 'chain 'F' and resid 203 through 204' Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 225 through 236 removed outlier: 4.124A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL F 230 " --> pdb=" O PRO F 226 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER F 231 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE F 236 " --> pdb=" O ILE F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 254 through 270 removed outlier: 4.233A pdb=" N LEU F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 290 removed outlier: 4.327A pdb=" N THR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 295 through 318 removed outlier: 3.535A pdb=" N MET F 301 " --> pdb=" O SER F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 354 removed outlier: 3.812A pdb=" N MET F 350 " --> pdb=" O GLY F 346 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 351 " --> pdb=" O GLY F 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.826A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.599A pdb=" N GLU A 120 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.591A pdb=" N LEU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 204 No H-bonds generated for 'chain 'A' and resid 203 through 204' Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.882A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.662A pdb=" N ASN A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 270 removed outlier: 4.302A pdb=" N LEU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 297 through 318 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.039A pdb=" N MET A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.617A pdb=" N LYS B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.569A pdb=" N VAL B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.590A pdb=" N VAL B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.585A pdb=" N CYS B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 204 No H-bonds generated for 'chain 'B' and resid 203 through 204' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 225 through 236 removed outlier: 4.119A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 254 through 270 removed outlier: 4.261A pdb=" N LEU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.515A pdb=" N ARG B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.662A pdb=" N MET B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.754A pdb=" N LYS B 214 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL B 278 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 216 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ASP B 280 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE B 218 " --> pdb=" O ASP B 280 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 180 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LEU B 358 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU B 182 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE B 360 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 184 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N LYS B 362 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 357 " --> pdb=" O VAL B 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 391 through 393 removed outlier: 6.459A pdb=" N ARG C 357 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 277 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR C 324 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL C 279 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C 216 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP C 280 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 218 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AA5, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA6, first strand: chain 'D' and resid 391 through 393 removed outlier: 6.477A pdb=" N ARG D 357 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE D 180 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU D 358 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU D 182 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE D 360 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE D 184 " --> pdb=" O PHE D 360 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N LYS D 362 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR D 181 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN D 325 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 183 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER D 275 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL D 322 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 277 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N THR D 324 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL D 279 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS D 214 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE D 277 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU D 216 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 279 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE D 218 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AA8, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'E' and resid 391 through 393 removed outlier: 6.501A pdb=" N ARG E 357 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE E 180 " --> pdb=" O THR E 356 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU E 358 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU E 182 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE E 360 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE E 184 " --> pdb=" O PHE E 360 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N LYS E 362 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR E 181 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASN E 325 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU E 183 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E 277 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR E 324 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 279 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU E 216 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASP E 280 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 218 " --> pdb=" O ASP E 280 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS E 215 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA E 250 " --> pdb=" O CYS E 215 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR E 217 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AB2, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AB3, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.442A pdb=" N CYS F 215 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA F 250 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR F 217 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS F 214 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE F 277 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 216 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL F 279 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE F 218 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER F 275 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL F 322 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE F 277 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR F 324 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL F 279 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR F 181 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASN F 325 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU F 183 " --> pdb=" O ASN F 325 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE F 180 " --> pdb=" O THR F 356 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU F 358 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU F 182 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE F 360 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE F 184 " --> pdb=" O PHE F 360 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N LYS F 362 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG F 357 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 327 through 329 Processing sheet with id=AB5, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AB6, first strand: chain 'A' and resid 391 through 393 removed outlier: 3.613A pdb=" N CYS A 370 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 357 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 180 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU A 358 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A 182 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE A 360 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 184 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N LYS A 362 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR A 181 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ASN A 325 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 183 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER A 275 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL A 322 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 277 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR A 324 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 279 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A 214 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL A 278 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 216 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASP A 280 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 218 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS A 215 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ALA A 250 " --> pdb=" O CYS A 215 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR A 217 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AB8, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'B' and resid 327 through 329 611 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3906 1.33 - 1.45: 2482 1.45 - 1.57: 8390 1.57 - 1.70: 83 1.70 - 1.82: 156 Bond restraints: 15017 Sorted by residual: bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 15012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 19806 1.84 - 3.67: 467 3.67 - 5.51: 65 5.51 - 7.35: 26 7.35 - 9.18: 2 Bond angle restraints: 20366 Sorted by residual: angle pdb=" C ASP E 280 " pdb=" N SER E 281 " pdb=" CA SER E 281 " ideal model delta sigma weight residual 121.70 128.18 -6.48 1.80e+00 3.09e-01 1.29e+01 angle pdb=" C ASP C 280 " pdb=" N SER C 281 " pdb=" CA SER C 281 " ideal model delta sigma weight residual 121.70 128.03 -6.33 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C ASP D 280 " pdb=" N SER D 281 " pdb=" CA SER D 281 " ideal model delta sigma weight residual 121.70 127.50 -5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" C ASP F 280 " pdb=" N SER F 281 " pdb=" CA SER F 281 " ideal model delta sigma weight residual 121.70 127.43 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" PA ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sigma weight residual 120.50 129.68 -9.18 3.00e+00 1.11e-01 9.37e+00 ... (remaining 20361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 8466 34.06 - 68.11: 523 68.11 - 102.17: 26 102.17 - 136.22: 5 136.22 - 170.28: 13 Dihedral angle restraints: 9033 sinusoidal: 3771 harmonic: 5262 Sorted by residual: dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual 300.00 129.72 170.28 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 131.60 168.40 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 133.77 166.23 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 9030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1351 0.030 - 0.060: 637 0.060 - 0.089: 187 0.089 - 0.119: 139 0.119 - 0.149: 32 Chirality restraints: 2346 Sorted by residual: chirality pdb=" CA ILE E 387 " pdb=" N ILE E 387 " pdb=" C ILE E 387 " pdb=" CB ILE E 387 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE D 387 " pdb=" N ILE D 387 " pdb=" C ILE D 387 " pdb=" CB ILE D 387 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE F 124 " pdb=" N ILE F 124 " pdb=" C ILE F 124 " pdb=" CB ILE F 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2343 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 297 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C SER A 297 " 0.056 2.00e-02 2.50e+03 pdb=" O SER A 297 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA A 298 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 239 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO A 240 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 225 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO C 226 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " 0.023 5.00e-02 4.00e+02 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 46 2.52 - 3.12: 9662 3.12 - 3.71: 20489 3.71 - 4.31: 30851 4.31 - 4.90: 51373 Nonbonded interactions: 112421 Sorted by model distance: nonbonded pdb=" O2B ADP D 501 " pdb=" F1 AF3 D 502 " model vdw 1.929 2.990 nonbonded pdb=" O2B ADP E 501 " pdb=" F1 AF3 E 502 " model vdw 1.957 2.990 nonbonded pdb=" O2B ADP C 501 " pdb=" F3 AF3 C 502 " model vdw 1.997 2.990 nonbonded pdb=" O2B ADP F 501 " pdb=" F1 AF3 F 502 " model vdw 2.003 2.990 nonbonded pdb=" O1B ADP B 501 " pdb="MG MG B 503 " model vdw 2.010 2.170 ... (remaining 112416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 7.780 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 1.670 Process input model: 36.020 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 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 : 0.010 0.602 15021 Z= 1.001 Angle : 0.692 9.185 20366 Z= 0.355 Chirality : 0.044 0.149 2346 Planarity : 0.004 0.063 2532 Dihedral : 20.733 170.279 5649 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.66 % Allowed : 21.85 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.27 (0.19), residues: 1830 helix: 0.30 (0.19), residues: 810 sheet: 2.63 (0.35), residues: 210 loop : -1.46 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 302 PHE 0.011 0.002 PHE B 385 TYR 0.010 0.002 TYR C 217 ARG 0.003 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.20116 ( 611) hydrogen bonds : angle 5.68443 ( 1710) covalent geometry : bond 0.00345 (15017) covalent geometry : angle 0.69209 (20366) Misc. bond : bond 0.60222 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.526 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 39 residues processed: 197 average time/residue: 1.6147 time to fit residues: 343.5757 Evaluate side-chains 196 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 383 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 GLN F 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111130 restraints weight = 13030.180| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.34 r_work: 0.2970 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15021 Z= 0.205 Angle : 0.729 7.643 20366 Z= 0.379 Chirality : 0.047 0.195 2346 Planarity : 0.005 0.057 2532 Dihedral : 16.692 160.581 2370 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.85 % Allowed : 19.59 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.22 (0.19), residues: 1830 helix: 0.29 (0.19), residues: 864 sheet: 2.87 (0.35), residues: 210 loop : -1.57 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 302 PHE 0.011 0.002 PHE B 385 TYR 0.010 0.002 TYR C 217 ARG 0.005 0.001 ARG C 293 Details of bonding type rmsd hydrogen bonds : bond 0.07826 ( 611) hydrogen bonds : angle 4.55329 ( 1710) covalent geometry : bond 0.00371 (15017) covalent geometry : angle 0.72937 (20366) Misc. bond : bond 0.00103 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7849 (mtm) REVERT: C 152 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7691 (ttm) REVERT: C 207 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7516 (p0) REVERT: C 343 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8931 (pttp) REVERT: D 115 ARG cc_start: 0.8161 (ttt180) cc_final: 0.7750 (ttt180) REVERT: D 126 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.6011 (mm-30) REVERT: D 188 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.6454 (ptt-90) REVERT: D 216 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8702 (tt) REVERT: E 115 ARG cc_start: 0.7896 (ttt-90) cc_final: 0.7651 (ttt-90) REVERT: E 138 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7294 (ttt180) REVERT: F 85 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6659 (mttm) REVERT: F 364 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6963 (ptpp) REVERT: A 93 MET cc_start: 0.5114 (OUTLIER) cc_final: 0.4031 (tmt) REVERT: A 204 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5904 (mp) outliers start: 58 outliers final: 23 residues processed: 207 average time/residue: 1.6457 time to fit residues: 367.1828 Evaluate side-chains 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 GLN E 267 GLN F 166 ASN A 245 ASN B 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111224 restraints weight = 13047.088| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.32 r_work: 0.2976 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15021 Z= 0.206 Angle : 0.729 7.564 20366 Z= 0.379 Chirality : 0.047 0.191 2346 Planarity : 0.005 0.056 2532 Dihedral : 16.479 156.421 2330 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.32 % Allowed : 19.46 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.20 (0.19), residues: 1830 helix: 0.30 (0.18), residues: 864 sheet: 2.95 (0.35), residues: 210 loop : -1.56 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 302 PHE 0.012 0.002 PHE B 184 TYR 0.010 0.002 TYR C 217 ARG 0.005 0.000 ARG C 293 Details of bonding type rmsd hydrogen bonds : bond 0.07727 ( 611) hydrogen bonds : angle 4.45757 ( 1710) covalent geometry : bond 0.00371 (15017) covalent geometry : angle 0.72883 (20366) Misc. bond : bond 0.00124 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 161 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5191 (mmp) REVERT: C 142 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7851 (mtm) REVERT: C 152 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7640 (ttm) REVERT: C 207 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7537 (p0) REVERT: C 343 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8913 (pttp) REVERT: D 115 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7898 (ttt180) REVERT: D 126 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5958 (mm-30) REVERT: D 188 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6400 (ptt-90) REVERT: D 216 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8713 (tt) REVERT: D 343 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8793 (ptpt) REVERT: F 93 MET cc_start: 0.5323 (mpt) cc_final: 0.4455 (mtm) REVERT: F 364 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6943 (ptpp) REVERT: A 93 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4060 (tmt) REVERT: A 204 ILE cc_start: 0.6184 (OUTLIER) cc_final: 0.5926 (mp) REVERT: B 115 ARG cc_start: 0.7036 (tmm-80) cc_final: 0.6636 (ttt-90) REVERT: B 142 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7256 (mtm) outliers start: 65 outliers final: 26 residues processed: 206 average time/residue: 1.7149 time to fit residues: 379.6126 Evaluate side-chains 198 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.147473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105780 restraints weight = 12853.760| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.31 r_work: 0.2899 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15021 Z= 0.372 Angle : 1.026 12.565 20366 Z= 0.541 Chirality : 0.059 0.264 2346 Planarity : 0.007 0.111 2532 Dihedral : 17.029 167.082 2328 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.18 % Allowed : 19.32 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.69 (0.19), residues: 1830 helix: -0.21 (0.18), residues: 864 sheet: 2.67 (0.34), residues: 210 loop : -1.66 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 302 PHE 0.017 0.003 PHE A 385 TYR 0.015 0.003 TYR F 217 ARG 0.008 0.001 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.11407 ( 611) hydrogen bonds : angle 4.90779 ( 1710) covalent geometry : bond 0.00725 (15017) covalent geometry : angle 1.02582 (20366) Misc. bond : bond 0.00244 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.5235 (mmp) REVERT: C 142 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7859 (mtm) REVERT: C 207 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7687 (p0) REVERT: C 293 ARG cc_start: 0.7401 (mpt180) cc_final: 0.6739 (tmm160) REVERT: C 343 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8904 (pttp) REVERT: D 115 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8052 (ttt90) REVERT: D 142 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7615 (mtm) REVERT: D 216 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8772 (tt) REVERT: D 263 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: D 287 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7231 (mtt-85) REVERT: D 343 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8783 (ptpt) REVERT: E 269 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7856 (mtt) REVERT: F 85 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6728 (mttm) REVERT: F 115 ARG cc_start: 0.7708 (ttt-90) cc_final: 0.7429 (ttt-90) REVERT: F 364 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7156 (ptpp) REVERT: A 93 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.4161 (tmt) REVERT: A 157 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.5303 (mp) REVERT: A 204 ILE cc_start: 0.6336 (OUTLIER) cc_final: 0.6130 (mp) outliers start: 63 outliers final: 24 residues processed: 202 average time/residue: 1.7252 time to fit residues: 374.2521 Evaluate side-chains 194 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 120 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 0.0570 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN F 166 ASN A 245 ASN B 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.157305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117275 restraints weight = 13329.140| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.34 r_work: 0.3069 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15021 Z= 0.133 Angle : 0.610 6.835 20366 Z= 0.311 Chirality : 0.042 0.163 2346 Planarity : 0.004 0.045 2532 Dihedral : 15.987 158.435 2324 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.59 % Allowed : 21.18 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.04 (0.20), residues: 1830 helix: 0.43 (0.19), residues: 870 sheet: 2.66 (0.31), residues: 270 loop : -1.61 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 257 PHE 0.013 0.001 PHE F 187 TYR 0.007 0.001 TYR B 253 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 611) hydrogen bonds : angle 4.07130 ( 1710) covalent geometry : bond 0.00241 (15017) covalent geometry : angle 0.61046 (20366) Misc. bond : bond 0.00076 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: C 293 ARG cc_start: 0.6724 (tpt170) cc_final: 0.6235 (tmm160) REVERT: D 115 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7769 (ttt90) REVERT: D 126 GLU cc_start: 0.6195 (OUTLIER) cc_final: 0.5980 (mm-30) REVERT: D 216 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8570 (tt) REVERT: F 93 MET cc_start: 0.5299 (mpt) cc_final: 0.4458 (mtm) REVERT: F 115 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.6952 (ttm-80) REVERT: F 122 LYS cc_start: 0.5339 (OUTLIER) cc_final: 0.4609 (ttmt) REVERT: F 364 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6886 (ptpp) REVERT: A 93 MET cc_start: 0.5129 (OUTLIER) cc_final: 0.4037 (tmt) REVERT: A 204 ILE cc_start: 0.6046 (OUTLIER) cc_final: 0.5786 (mp) outliers start: 39 outliers final: 13 residues processed: 192 average time/residue: 1.6776 time to fit residues: 346.4537 Evaluate side-chains 172 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.154906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.114321 restraints weight = 13169.812| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.34 r_work: 0.3024 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15021 Z= 0.160 Angle : 0.648 7.236 20366 Z= 0.333 Chirality : 0.044 0.163 2346 Planarity : 0.004 0.044 2532 Dihedral : 15.989 156.998 2322 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.32 % Allowed : 21.91 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.14 (0.20), residues: 1830 helix: 0.51 (0.19), residues: 870 sheet: 2.70 (0.31), residues: 270 loop : -1.56 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 257 PHE 0.011 0.001 PHE B 184 TYR 0.008 0.001 TYR B 253 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.06034 ( 611) hydrogen bonds : angle 4.12872 ( 1710) covalent geometry : bond 0.00287 (15017) covalent geometry : angle 0.64845 (20366) Misc. bond : bond 0.00103 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: C 293 ARG cc_start: 0.6950 (tpt170) cc_final: 0.6383 (tmm160) REVERT: C 343 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8913 (pttp) REVERT: D 115 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7969 (ttt180) REVERT: D 126 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5940 (mm-30) REVERT: D 216 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8647 (tt) REVERT: E 138 ARG cc_start: 0.7662 (ttp-110) cc_final: 0.7421 (ttt180) REVERT: F 93 MET cc_start: 0.5345 (mpt) cc_final: 0.4508 (mtm) REVERT: F 115 ARG cc_start: 0.7679 (ttt-90) cc_final: 0.7017 (ttm-80) REVERT: F 122 LYS cc_start: 0.5328 (OUTLIER) cc_final: 0.4560 (ttmt) REVERT: F 364 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6859 (ptpp) REVERT: A 93 MET cc_start: 0.5189 (OUTLIER) cc_final: 0.4084 (tmt) REVERT: A 204 ILE cc_start: 0.6104 (OUTLIER) cc_final: 0.5814 (mp) REVERT: B 216 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8884 (tp) outliers start: 35 outliers final: 18 residues processed: 186 average time/residue: 1.8219 time to fit residues: 363.8669 Evaluate side-chains 182 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 171 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112249 restraints weight = 13223.556| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.34 r_work: 0.2989 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15021 Z= 0.186 Angle : 0.693 7.447 20366 Z= 0.358 Chirality : 0.045 0.170 2346 Planarity : 0.004 0.047 2532 Dihedral : 16.150 156.572 2321 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.86 % Allowed : 21.38 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.07 (0.20), residues: 1830 helix: 0.45 (0.18), residues: 870 sheet: 2.67 (0.31), residues: 270 loop : -1.58 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 302 PHE 0.011 0.002 PHE B 184 TYR 0.009 0.001 TYR C 217 ARG 0.006 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.06968 ( 611) hydrogen bonds : angle 4.25417 ( 1710) covalent geometry : bond 0.00335 (15017) covalent geometry : angle 0.69344 (20366) Misc. bond : bond 0.00125 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.849 Fit side-chains revert: symmetry clash REVERT: C 142 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7897 (mtm) REVERT: C 293 ARG cc_start: 0.7070 (tpt170) cc_final: 0.6525 (tmm160) REVERT: C 343 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8927 (pttp) REVERT: D 126 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.6003 (mm-30) REVERT: D 216 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8703 (tt) REVERT: E 138 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7395 (ttt180) REVERT: F 93 MET cc_start: 0.5270 (mpt) cc_final: 0.4421 (mtm) REVERT: F 115 ARG cc_start: 0.7653 (ttt-90) cc_final: 0.6997 (ttm-80) REVERT: F 122 LYS cc_start: 0.5253 (OUTLIER) cc_final: 0.4501 (ttmt) REVERT: F 130 ASP cc_start: 0.6410 (m-30) cc_final: 0.5612 (m-30) REVERT: F 364 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6915 (ptpp) REVERT: A 93 MET cc_start: 0.5125 (OUTLIER) cc_final: 0.3990 (tmt) REVERT: A 204 ILE cc_start: 0.6032 (OUTLIER) cc_final: 0.5800 (mp) outliers start: 43 outliers final: 19 residues processed: 197 average time/residue: 1.7039 time to fit residues: 362.1464 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 83 optimal weight: 0.0470 chunk 86 optimal weight: 3.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.149491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108132 restraints weight = 13013.575| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.33 r_work: 0.2925 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15021 Z= 0.288 Angle : 0.878 10.148 20366 Z= 0.461 Chirality : 0.052 0.218 2346 Planarity : 0.006 0.074 2532 Dihedral : 16.675 164.277 2321 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.72 % Allowed : 21.38 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.35 (0.19), residues: 1830 helix: 0.19 (0.18), residues: 852 sheet: 2.89 (0.34), residues: 210 loop : -1.64 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 302 PHE 0.014 0.002 PHE A 385 TYR 0.013 0.002 TYR F 217 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.09691 ( 611) hydrogen bonds : angle 4.64671 ( 1710) covalent geometry : bond 0.00544 (15017) covalent geometry : angle 0.87799 (20366) Misc. bond : bond 0.00196 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: C 142 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7922 (mtm) REVERT: C 293 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6761 (tmm160) REVERT: C 343 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8925 (pttp) REVERT: D 216 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8745 (tt) REVERT: D 263 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: E 138 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.7364 (ttt180) REVERT: F 85 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6698 (mttm) REVERT: F 115 ARG cc_start: 0.7639 (ttt-90) cc_final: 0.7197 (ttt-90) REVERT: F 364 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.7061 (ptpp) REVERT: A 93 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4066 (tmt) REVERT: A 204 ILE cc_start: 0.6145 (OUTLIER) cc_final: 0.5905 (mp) REVERT: B 120 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6963 (mt-10) outliers start: 41 outliers final: 24 residues processed: 192 average time/residue: 1.6875 time to fit residues: 347.8506 Evaluate side-chains 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 0.0050 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN E 267 GLN F 166 ASN A 245 ASN B 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.155137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114774 restraints weight = 13131.699| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.31 r_work: 0.3028 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15021 Z= 0.154 Angle : 0.648 8.105 20366 Z= 0.333 Chirality : 0.043 0.164 2346 Planarity : 0.004 0.046 2532 Dihedral : 16.081 157.723 2321 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.06 % Allowed : 21.91 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.06 (0.20), residues: 1830 helix: 0.50 (0.19), residues: 858 sheet: 2.66 (0.31), residues: 270 loop : -1.65 (0.20), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 302 PHE 0.011 0.001 PHE B 184 TYR 0.008 0.001 TYR C 253 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.05813 ( 611) hydrogen bonds : angle 4.18622 ( 1710) covalent geometry : bond 0.00277 (15017) covalent geometry : angle 0.64823 (20366) Misc. bond : bond 0.00106 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: C 293 ARG cc_start: 0.6901 (tpt170) cc_final: 0.6422 (tmm160) REVERT: C 343 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8914 (pttp) REVERT: D 115 ARG cc_start: 0.8198 (ttt180) cc_final: 0.7794 (ttt90) REVERT: D 126 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6005 (mm-30) REVERT: D 216 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8647 (tt) REVERT: E 138 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.7405 (ttt180) REVERT: F 93 MET cc_start: 0.5275 (mpt) cc_final: 0.4414 (mtm) REVERT: F 115 ARG cc_start: 0.7606 (ttt-90) cc_final: 0.7149 (ttt-90) REVERT: F 122 LYS cc_start: 0.5250 (OUTLIER) cc_final: 0.4541 (ttmt) REVERT: F 130 ASP cc_start: 0.6368 (m-30) cc_final: 0.6097 (m-30) REVERT: F 364 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6891 (ptpp) REVERT: A 93 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4011 (tmt) REVERT: A 204 ILE cc_start: 0.5993 (OUTLIER) cc_final: 0.5731 (mp) REVERT: B 115 ARG cc_start: 0.6984 (tmm-80) cc_final: 0.6603 (ttt-90) REVERT: B 142 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7202 (mtm) outliers start: 31 outliers final: 18 residues processed: 186 average time/residue: 1.7643 time to fit residues: 351.9390 Evaluate side-chains 184 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN E 267 GLN F 166 ASN A 245 ASN B 267 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118649 restraints weight = 13439.606| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.22 r_work: 0.3083 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15021 Z= 0.135 Angle : 0.612 8.660 20366 Z= 0.311 Chirality : 0.042 0.147 2346 Planarity : 0.004 0.044 2532 Dihedral : 15.732 157.844 2321 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.86 % Allowed : 22.24 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.31 (0.20), residues: 1830 helix: 0.68 (0.19), residues: 864 sheet: 2.82 (0.31), residues: 270 loop : -1.52 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 257 PHE 0.011 0.001 PHE B 184 TYR 0.007 0.001 TYR B 253 ARG 0.007 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 611) hydrogen bonds : angle 4.04378 ( 1710) covalent geometry : bond 0.00246 (15017) covalent geometry : angle 0.61229 (20366) Misc. bond : bond 0.00093 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: C 293 ARG cc_start: 0.6982 (tpt170) cc_final: 0.6319 (tmm160) REVERT: D 115 ARG cc_start: 0.8296 (ttt180) cc_final: 0.7949 (ttt90) REVERT: D 216 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8618 (tt) REVERT: E 138 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7526 (ttt180) REVERT: F 93 MET cc_start: 0.5376 (mpt) cc_final: 0.4548 (mtm) REVERT: F 115 ARG cc_start: 0.7654 (ttt-90) cc_final: 0.7220 (ttt-90) REVERT: F 122 LYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4620 (ttmt) REVERT: F 128 LYS cc_start: 0.5666 (ptpt) cc_final: 0.4915 (ptpt) REVERT: F 130 ASP cc_start: 0.6484 (m-30) cc_final: 0.6258 (m-30) REVERT: F 364 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6874 (ptpp) REVERT: A 93 MET cc_start: 0.5168 (OUTLIER) cc_final: 0.3957 (tmt) REVERT: A 204 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5780 (mp) REVERT: A 241 ASP cc_start: 0.5899 (m-30) cc_final: 0.5558 (m-30) REVERT: B 115 ARG cc_start: 0.7019 (tmm-80) cc_final: 0.6660 (ttt-90) REVERT: B 142 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7220 (mtm) outliers start: 28 outliers final: 16 residues processed: 184 average time/residue: 1.7256 time to fit residues: 340.2572 Evaluate side-chains 182 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 152 optimal weight: 0.0270 chunk 170 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.157345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118446 restraints weight = 13349.924| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.22 r_work: 0.3082 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15021 Z= 0.135 Angle : 0.611 8.601 20366 Z= 0.310 Chirality : 0.042 0.145 2346 Planarity : 0.004 0.043 2532 Dihedral : 15.546 158.193 2318 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.66 % Allowed : 22.44 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1830 helix: 0.76 (0.19), residues: 864 sheet: 2.87 (0.31), residues: 270 loop : -1.50 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 257 PHE 0.011 0.001 PHE B 184 TYR 0.007 0.001 TYR B 253 ARG 0.007 0.000 ARG E 115 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 611) hydrogen bonds : angle 4.01445 ( 1710) covalent geometry : bond 0.00247 (15017) covalent geometry : angle 0.61072 (20366) Misc. bond : bond 0.00092 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14399.88 seconds wall clock time: 250 minutes 22.88 seconds (15022.88 seconds total)