Starting phenix.real_space_refine on Thu Sep 18 06:47:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2d_44104/09_2025/9b2d_44104_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2d_44104/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b2d_44104/09_2025/9b2d_44104_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2d_44104/09_2025/9b2d_44104_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b2d_44104/09_2025/9b2d_44104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2d_44104/09_2025/9b2d_44104.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.83, per 1000 atoms: 0.26 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: 1.32 Conformation dependent library (CDL) restraints added in 675.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 1.88 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: 2.60 Time building geometry restraints manager: 1.67 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: 8.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.650 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.320 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 225 TYR 0.010 0.002 TYR C 217 PHE 0.011 0.002 PHE B 385 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00345 (15017) covalent geometry : angle 0.69209 (20366) hydrogen bonds : bond 0.20116 ( 611) hydrogen bonds : angle 5.68443 ( 1710) 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 : 0.646 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 39 residues processed: 197 average time/residue: 0.8548 time to fit residues: 180.9182 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 : 0.682 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 GLN ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.108530 restraints weight = 13021.143| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.35 r_work: 0.2934 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15021 Z= 0.268 Angle : 0.843 8.593 20366 Z= 0.442 Chirality : 0.051 0.224 2346 Planarity : 0.006 0.080 2532 Dihedral : 16.944 163.779 2370 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.19), residues: 1830 helix: 0.06 (0.18), residues: 864 sheet: 2.76 (0.35), residues: 210 loop : -1.61 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 293 TYR 0.011 0.002 TYR F 217 PHE 0.013 0.002 PHE A 385 HIS 0.005 0.002 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00499 (15017) covalent geometry : angle 0.84262 (20366) hydrogen bonds : bond 0.09550 ( 611) hydrogen bonds : angle 4.77395 ( 1710) Misc. bond : bond 0.00110 ( 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 222 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 157 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: C 142 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: C 152 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7663 (ttm) REVERT: C 343 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8912 (pttp) REVERT: D 216 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8753 (tt) REVERT: D 287 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7950 (mtt-85) REVERT: E 115 ARG cc_start: 0.7926 (ttt-90) cc_final: 0.7721 (ttt-90) REVERT: F 85 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6699 (mttm) REVERT: F 115 ARG cc_start: 0.7710 (ttt-90) cc_final: 0.7400 (ttt-90) REVERT: F 364 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.7005 (ptpp) REVERT: A 93 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4101 (tmt) REVERT: A 204 ILE cc_start: 0.6292 (OUTLIER) cc_final: 0.6037 (mp) REVERT: B 142 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7330 (mtm) outliers start: 65 outliers final: 28 residues processed: 204 average time/residue: 0.9168 time to fit residues: 199.9353 Evaluate side-chains 194 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 126 GLU 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 287 ARG 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 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 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 149 ASP 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 216 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 88 VAL 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 281 SER 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 93 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.152543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111498 restraints weight = 13246.518| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.35 r_work: 0.2977 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15021 Z= 0.189 Angle : 0.704 7.418 20366 Z= 0.365 Chirality : 0.046 0.185 2346 Planarity : 0.005 0.046 2532 Dihedral : 16.357 156.759 2327 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.98 % Allowed : 19.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.19), residues: 1830 helix: 0.29 (0.18), residues: 864 sheet: 2.90 (0.35), residues: 210 loop : -1.58 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.009 0.001 TYR C 217 PHE 0.012 0.002 PHE B 184 HIS 0.004 0.001 HIS C 302 Details of bonding type rmsd covalent geometry : bond 0.00337 (15017) covalent geometry : angle 0.70421 (20366) hydrogen bonds : bond 0.07206 ( 611) hydrogen bonds : angle 4.42020 ( 1710) Misc. bond : bond 0.00116 ( 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 221 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5136 (mmp) REVERT: C 152 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7691 (ttm) REVERT: C 343 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8933 (pttp) REVERT: D 115 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7884 (ttt90) REVERT: D 126 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.6010 (mm-30) REVERT: D 216 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8687 (tt) REVERT: D 343 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8839 (ptpt) REVERT: F 93 MET cc_start: 0.5341 (mpt) cc_final: 0.4490 (mtm) REVERT: F 128 LYS cc_start: 0.5498 (ptpt) cc_final: 0.5291 (ptpt) REVERT: F 364 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6971 (ptpp) REVERT: A 93 MET cc_start: 0.5101 (OUTLIER) cc_final: 0.4037 (tmt) REVERT: A 204 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5903 (mp) outliers start: 60 outliers final: 25 residues processed: 206 average time/residue: 0.8686 time to fit residues: 191.8966 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 : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 270 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 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 124 ILE 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 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 74 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 A 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110989 restraints weight = 13096.491| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.35 r_work: 0.2970 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0792 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= 0.204 Angle : 0.728 7.566 20366 Z= 0.378 Chirality : 0.047 0.187 2346 Planarity : 0.005 0.047 2532 Dihedral : 16.351 156.255 2323 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.45 % Allowed : 20.45 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.19), residues: 1830 helix: 0.31 (0.18), residues: 864 sheet: 2.96 (0.35), residues: 210 loop : -1.58 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.010 0.002 TYR C 217 PHE 0.012 0.002 PHE B 184 HIS 0.004 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00368 (15017) covalent geometry : angle 0.72769 (20366) hydrogen bonds : bond 0.07633 ( 611) hydrogen bonds : angle 4.42788 ( 1710) Misc. bond : bond 0.00131 ( 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 214 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.5225 (mmp) REVERT: C 152 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7619 (ttm) REVERT: C 293 ARG cc_start: 0.7006 (mpt180) cc_final: 0.6439 (tmm160) REVERT: C 343 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8913 (pttp) REVERT: D 115 ARG cc_start: 0.8216 (ttt180) cc_final: 0.7842 (ttt90) REVERT: D 126 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.6005 (mm-30) REVERT: D 142 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7503 (mtm) REVERT: D 216 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8713 (tt) REVERT: D 343 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8798 (ptpt) REVERT: F 115 ARG cc_start: 0.7678 (ttt-90) cc_final: 0.6940 (ttm-80) REVERT: F 364 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6950 (ptpp) REVERT: A 93 MET cc_start: 0.5149 (OUTLIER) cc_final: 0.4058 (tmt) REVERT: A 204 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.5950 (mp) outliers start: 52 outliers final: 27 residues processed: 197 average time/residue: 0.9084 time to fit residues: 191.5006 Evaluate side-chains 192 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 152 MET 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 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 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 124 ILE 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 A residue 378 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.153160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112128 restraints weight = 13161.626| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.35 r_work: 0.2988 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15021 Z= 0.186 Angle : 0.696 7.421 20366 Z= 0.360 Chirality : 0.045 0.181 2346 Planarity : 0.004 0.047 2532 Dihedral : 16.232 156.680 2323 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.92 % Allowed : 20.12 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.20), residues: 1830 helix: 0.37 (0.18), residues: 870 sheet: 2.57 (0.31), residues: 270 loop : -1.63 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.009 0.001 TYR C 217 PHE 0.012 0.002 PHE B 184 HIS 0.003 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00334 (15017) covalent geometry : angle 0.69601 (20366) hydrogen bonds : bond 0.07010 ( 611) hydrogen bonds : angle 4.32541 ( 1710) Misc. bond : bond 0.00123 ( 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 217 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.5105 (mmp) REVERT: C 152 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7612 (ttm) REVERT: C 293 ARG cc_start: 0.6980 (mpt180) cc_final: 0.6485 (tmm160) REVERT: C 343 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8920 (pttp) REVERT: D 126 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.6061 (mm-30) REVERT: D 216 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8685 (tt) REVERT: E 216 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8492 (tt) REVERT: F 93 MET cc_start: 0.5258 (mpt) cc_final: 0.4413 (mtm) REVERT: F 115 ARG cc_start: 0.7673 (ttt-90) cc_final: 0.7173 (ttt-90) REVERT: F 364 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6941 (ptpp) REVERT: A 93 MET cc_start: 0.5101 (OUTLIER) cc_final: 0.4026 (tmt) REVERT: A 204 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5894 (mp) REVERT: B 115 ARG cc_start: 0.7025 (tmm-80) cc_final: 0.6636 (ttt-90) REVERT: B 142 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7276 (mtm) outliers start: 59 outliers final: 30 residues processed: 201 average time/residue: 0.8555 time to fit residues: 184.4736 Evaluate side-chains 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 270 SER 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 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 216 LEU 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 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 A residue 378 LEU Chi-restraints excluded: chain B residue 79 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 66 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 A 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110155 restraints weight = 13039.901| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.34 r_work: 0.2959 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15021 Z= 0.225 Angle : 0.765 7.711 20366 Z= 0.399 Chirality : 0.048 0.195 2346 Planarity : 0.005 0.051 2532 Dihedral : 16.450 158.547 2323 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.45 % Allowed : 20.72 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.19), residues: 1830 helix: 0.28 (0.18), residues: 864 sheet: 2.94 (0.35), residues: 210 loop : -1.58 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.010 0.002 TYR C 217 PHE 0.012 0.002 PHE B 184 HIS 0.004 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00411 (15017) covalent geometry : angle 0.76511 (20366) hydrogen bonds : bond 0.08206 ( 611) hydrogen bonds : angle 4.47379 ( 1710) Misc. bond : bond 0.00150 ( 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 212 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.5146 (mmp) REVERT: C 152 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7611 (ttm) REVERT: C 207 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7533 (p0) REVERT: C 293 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6639 (tmm160) REVERT: C 343 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8925 (pttp) REVERT: D 115 ARG cc_start: 0.8236 (ttt180) cc_final: 0.7881 (ttt90) REVERT: D 126 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5960 (mm-30) REVERT: D 216 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8726 (tt) REVERT: E 216 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8500 (tt) REVERT: F 85 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6669 (mttm) REVERT: F 115 ARG cc_start: 0.7672 (ttt-90) cc_final: 0.7147 (ttt-90) REVERT: F 126 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.5307 (tm-30) REVERT: F 293 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7062 (ttm170) REVERT: F 364 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6963 (ptpp) REVERT: A 93 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4021 (tmt) REVERT: A 204 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5965 (mp) outliers start: 52 outliers final: 30 residues processed: 199 average time/residue: 0.8843 time to fit residues: 188.3292 Evaluate side-chains 200 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 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 126 GLU 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 288 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 216 LEU 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 79 SER 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 126 GLU 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 293 ARG 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 A residue 378 LEU Chi-restraints excluded: chain B residue 79 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 26 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 25 optimal weight: 0.0020 chunk 132 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 A 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.159133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119382 restraints weight = 13257.713| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.33 r_work: 0.3092 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15021 Z= 0.121 Angle : 0.584 6.848 20366 Z= 0.295 Chirality : 0.042 0.154 2346 Planarity : 0.004 0.041 2532 Dihedral : 15.742 159.112 2323 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.20), residues: 1830 helix: 0.68 (0.19), residues: 870 sheet: 2.81 (0.31), residues: 270 loop : -1.51 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.006 0.001 TYR C 253 PHE 0.013 0.001 PHE D 187 HIS 0.002 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00224 (15017) covalent geometry : angle 0.58425 (20366) hydrogen bonds : bond 0.04258 ( 611) hydrogen bonds : angle 3.89663 ( 1710) Misc. bond : bond 0.00085 ( 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 196 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: C 293 ARG cc_start: 0.6723 (tpt170) cc_final: 0.6128 (tmm160) REVERT: D 115 ARG cc_start: 0.8195 (ttt180) cc_final: 0.7880 (ttt90) REVERT: D 216 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8585 (tt) REVERT: E 116 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6983 (pttp) REVERT: E 138 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7235 (ttt-90) REVERT: F 93 MET cc_start: 0.5306 (mpt) cc_final: 0.4488 (mtm) REVERT: F 115 ARG cc_start: 0.7600 (ttt-90) cc_final: 0.7016 (ttm-80) REVERT: F 122 LYS cc_start: 0.5261 (OUTLIER) cc_final: 0.4547 (ttmt) REVERT: F 364 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6804 (ptpp) REVERT: A 93 MET cc_start: 0.5127 (OUTLIER) cc_final: 0.3972 (tmt) REVERT: A 116 LYS cc_start: 0.5446 (ttpt) cc_final: 0.5133 (ptpt) REVERT: A 204 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5761 (mp) REVERT: A 241 ASP cc_start: 0.5891 (m-30) cc_final: 0.5558 (m-30) REVERT: B 115 ARG cc_start: 0.6990 (tmm-80) cc_final: 0.6622 (ttt-90) REVERT: B 176 GLU cc_start: 0.7667 (tt0) cc_final: 0.7151 (tp30) outliers start: 31 outliers final: 13 residues processed: 189 average time/residue: 0.9447 time to fit residues: 190.3532 Evaluate side-chains 178 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 183 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 124 ILE 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 208 ILE 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 151 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 48 optimal weight: 0.1980 chunk 163 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.151348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110153 restraints weight = 13117.939| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.34 r_work: 0.2956 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 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 : 0.004 0.038 15021 Z= 0.219 Angle : 0.753 7.721 20366 Z= 0.391 Chirality : 0.047 0.190 2346 Planarity : 0.005 0.048 2532 Dihedral : 16.212 157.966 2314 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.99 % Allowed : 21.38 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.19), residues: 1830 helix: 0.45 (0.19), residues: 864 sheet: 3.06 (0.35), residues: 210 loop : -1.49 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.011 0.002 TYR C 217 PHE 0.011 0.002 PHE A 385 HIS 0.004 0.001 HIS E 302 Details of bonding type rmsd covalent geometry : bond 0.00401 (15017) covalent geometry : angle 0.75259 (20366) hydrogen bonds : bond 0.07936 ( 611) hydrogen bonds : angle 4.38013 ( 1710) Misc. bond : bond 0.00150 ( 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 210 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: C 293 ARG cc_start: 0.7169 (tpt170) cc_final: 0.6640 (tmm160) REVERT: C 343 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8961 (pttp) REVERT: D 115 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7998 (ttt90) REVERT: D 216 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8724 (tt) REVERT: D 343 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8778 (ptpt) REVERT: E 116 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7167 (pttp) REVERT: E 138 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7304 (ttt-90) REVERT: F 93 MET cc_start: 0.5277 (mpt) cc_final: 0.4438 (mtm) REVERT: F 115 ARG cc_start: 0.7623 (ttt-90) cc_final: 0.7028 (ttm-80) REVERT: F 122 LYS cc_start: 0.5249 (OUTLIER) cc_final: 0.4475 (ttmt) REVERT: F 364 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6984 (ptpp) REVERT: A 93 MET cc_start: 0.5075 (OUTLIER) cc_final: 0.3934 (tmt) REVERT: A 204 ILE cc_start: 0.6128 (OUTLIER) cc_final: 0.5874 (mp) outliers start: 45 outliers final: 19 residues processed: 199 average time/residue: 0.8816 time to fit residues: 187.7153 Evaluate side-chains 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 158 ILE 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 116 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 79 SER 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 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 79 SER Chi-restraints excluded: chain B residue 156 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 43 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.157556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118831 restraints weight = 13506.511| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.23 r_work: 0.3089 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15021 Z= 0.129 Angle : 0.602 7.893 20366 Z= 0.305 Chirality : 0.042 0.157 2346 Planarity : 0.004 0.042 2532 Dihedral : 15.681 158.285 2314 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.86 % Allowed : 22.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.20), residues: 1830 helix: 0.73 (0.19), residues: 864 sheet: 2.83 (0.31), residues: 270 loop : -1.51 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.007 0.001 TYR C 253 PHE 0.012 0.001 PHE D 187 HIS 0.002 0.001 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00236 (15017) covalent geometry : angle 0.60229 (20366) hydrogen bonds : bond 0.04745 ( 611) hydrogen bonds : angle 3.97134 ( 1710) Misc. bond : bond 0.00088 ( 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 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: C 293 ARG cc_start: 0.6885 (tpt170) cc_final: 0.6200 (ttp-110) REVERT: D 216 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8620 (tt) REVERT: E 138 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7365 (ttt-90) REVERT: F 93 MET cc_start: 0.5346 (mpt) cc_final: 0.4517 (mtm) REVERT: F 115 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7288 (ttt-90) REVERT: F 122 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.4609 (ttmt) REVERT: F 364 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6882 (ptpp) REVERT: A 93 MET cc_start: 0.5147 (OUTLIER) cc_final: 0.3982 (tmt) REVERT: A 116 LYS cc_start: 0.5478 (ttpt) cc_final: 0.5189 (ptpt) REVERT: A 204 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5828 (mp) REVERT: A 241 ASP cc_start: 0.5865 (m-30) cc_final: 0.5542 (m-30) REVERT: B 115 ARG cc_start: 0.7030 (tmm-80) cc_final: 0.6670 (ttt-90) REVERT: B 165 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7445 (mmpt) REVERT: B 176 GLU cc_start: 0.7692 (tt0) cc_final: 0.7202 (tp30) outliers start: 28 outliers final: 15 residues processed: 180 average time/residue: 0.9674 time to fit residues: 185.5972 Evaluate side-chains 181 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 270 SER 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 120 GLU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 124 ILE 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 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 22 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.154013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114825 restraints weight = 13234.610| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.73 r_work: 0.3024 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15021 Z= 0.169 Angle : 0.667 8.398 20366 Z= 0.343 Chirality : 0.044 0.157 2346 Planarity : 0.004 0.044 2532 Dihedral : 15.872 157.064 2314 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.99 % Allowed : 22.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1830 helix: 0.68 (0.19), residues: 858 sheet: 2.76 (0.31), residues: 270 loop : -1.53 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.008 0.001 TYR B 253 PHE 0.011 0.001 PHE B 184 HIS 0.003 0.001 HIS C 302 Details of bonding type rmsd covalent geometry : bond 0.00304 (15017) covalent geometry : angle 0.66747 (20366) hydrogen bonds : bond 0.06374 ( 611) hydrogen bonds : angle 4.22175 ( 1710) Misc. bond : bond 0.00111 ( 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 191 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: C 293 ARG cc_start: 0.7108 (tpt170) cc_final: 0.6531 (tmm160) REVERT: D 216 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8679 (tt) REVERT: D 343 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8784 (ptpt) REVERT: E 138 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7350 (ttt-90) REVERT: F 93 MET cc_start: 0.5362 (mpt) cc_final: 0.4505 (mtm) REVERT: F 115 ARG cc_start: 0.7679 (ttt-90) cc_final: 0.7071 (ttm-80) REVERT: F 122 LYS cc_start: 0.5200 (OUTLIER) cc_final: 0.4516 (ttmt) REVERT: F 364 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6927 (ptpp) REVERT: A 93 MET cc_start: 0.5158 (OUTLIER) cc_final: 0.3981 (tmt) REVERT: A 116 LYS cc_start: 0.5491 (ttpt) cc_final: 0.5196 (ptpt) REVERT: A 204 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5796 (mp) REVERT: A 241 ASP cc_start: 0.5931 (m-30) cc_final: 0.5609 (m-30) REVERT: B 115 ARG cc_start: 0.7107 (tmm-80) cc_final: 0.6744 (ttt-90) REVERT: B 176 GLU cc_start: 0.7706 (tt0) cc_final: 0.7201 (tp30) outliers start: 30 outliers final: 19 residues processed: 184 average time/residue: 0.9385 time to fit residues: 184.3372 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 270 SER 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 D residue 343 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 79 SER 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 79 SER Chi-restraints excluded: chain B residue 156 GLU 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 69 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 0.0050 chunk 173 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.157016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117956 restraints weight = 13402.493| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.25 r_work: 0.3077 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15021 Z= 0.134 Angle : 0.609 8.644 20366 Z= 0.309 Chirality : 0.042 0.157 2346 Planarity : 0.004 0.042 2532 Dihedral : 15.614 158.299 2314 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.59 % Allowed : 22.58 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 1830 helix: 0.77 (0.19), residues: 864 sheet: 2.87 (0.31), residues: 270 loop : -1.47 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 115 TYR 0.007 0.001 TYR C 253 PHE 0.011 0.001 PHE D 187 HIS 0.003 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00245 (15017) covalent geometry : angle 0.60892 (20366) hydrogen bonds : bond 0.04922 ( 611) hydrogen bonds : angle 4.03536 ( 1710) Misc. bond : bond 0.00091 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8180.99 seconds wall clock time: 139 minutes 30.42 seconds (8370.42 seconds total)